Gibberellin 2-Oxidase Genes And Uses Thereof

ABSTRACT

Novel gibberellin 2-oxidase (GA2ox) genes were identified. Differential expression of GA2ox genes correlated with flower development, seed germination, tiller growth and other developmental processes. In addition, the early and increased growth of tiller and adventitious root and altered root architecture caused by overexpression of GA2oxs further suggest the pleiotropic role of GA2oxs in controlling growth and architecture in plants such as rice. GA2ox5, GA2ox6 and GA2ox9 were three genes encoding class C20 GA2oxs in rice. Mutants or transgenic rice overexpressing class C20 GA2oxs exhibited a broad range of mutant phenotypes, including semi-dwarfism, increased root system and higher tiller numbers that may favor grain yield. Mutations in the conserved domain III were found to affect the physiological activity of class C20 GA2oxs.

BACKGROUND OF THE INVENTION

Gibberellins (GAs) are a class of essential hormones controlling a variety of growth and development processes during the entire life cycle of plants, including seed germination, apical dominance, leaf expansion, stem elongation, root growth, floral initiation, anther development and fruit maturation (Harberd et al., 1998; Ross et al., 1997; Hedden and Phillips, 2000, Kin and Evan, 2003, Sun and Gubler, 2004; Kende and Zeevaart, 1997, del Pozo, et al., 2005). GAs are substituted tetracyclic diterpene carboxylic acids formed over several biosynthetic steps (Hedden and Phillips, 2000). To date, 136 different GAs have been identified in plants, fungi and bacteria (see for example, the World Wide Web site of plant-hormones.info/gibberellins); however, most of these GAs are precursors or degradation products.

The bioactive GAs synthesized by higher plants are GA₁, GA₃, GA₄, and GA₇ (Hedden and Phillips, 2000). The GA biosynthetic pathway can be classified into three stages, with three classes of enzymes involved, including terpene cyclases, cytochrome P450 monooxygenases (CYP450s), and 2-oxoglutarate-dependent dioxygenases (2-ODDs, including GA 20-oxidase, GA 7-oxidase, GA 3-oxidase, and GA 2-oxidase) (Olszewski et al., 2002; Graebe, 1987, Hedden and Phillip, 2000, Sakamoto et al., 2004). Mutants defective in GA biosynthesis have been identified in a variety of plant species, with the most prominent phenotypes being reduced internode length and small dark green leaves (Koornneef and van der Veen, 1980). Other phenotypes include prolonged germination dormancy, inhibited root growth, defective flowering, reduced seed production, and male sterility (King and Evans, 2003, Sakamoto et al., 2004, Tanimoto, 2005, Wang and Li, 2005). Normal growth of these mutants can be restored by exogenous application of active GAs.

GA 2-oxidases (GA2oxs) are a class of 2-ODDs (Thomas, et al., 1999; Sakamoto, et al., 2001, Schomburg, et al., 2003, Sakamoto et al., 2004, Lee and Zeevaart, 2005). The class C19 GA2oxs identified in various plant species can hydroxylate the C-2 of active C₁₉-GAs (GA₁ and GA₄) or C₁₉-GA precursors (GA₂₀ and GA₉) to produce biologically inactive GAs (GA₈, GA₃₄, GA₂₉, and GA₅₁, respectively) (Sakamoto et al., 2004). Recently, three novel class C20 GA2oxs, including Arabidopsis GA2ox7 and GA2ox8 and spinach GA2ox3, were found to hydroxylate C₂₀-GA precursors (converting GA₁₂ and GA₅₃ to GA₁₁₀ and GA₉₇, respectively) but not C₁₉-GAs (Schomburg et al., 2003, Lee and Zeevaart, 2005). The 2β-hydroxylation of C₂₀-GA precursors to GA₁₁₀ and GA₉₇ renders them unable to be converted to active GAs and thus decreases active GA levels. The class C20 GA2oxs contain three unique and conserved amino acid domains that are absent in the class C19 GA2oxs (Lee and Zeevaart, 2005).

The physiological function of GA2oxs has been studied in a variety of plant species. Arabidopsis GA2ox1 and GA2ox2 were found to be expressed in inflorescences and developing siliques, which is consistent with a role of GA2oxs in reducing GA levels and promoting seed dormancy (Thomas et al., 1999). Further study with the pea slender mutant, where the SLENDER gene encoding a GA2ox had been knocked out, showed that GA level increased during germination, and resultant seedlings were hyperelongated (Martin et al., 1999). More recently, dwarf phenotype was also found to correlate with reduced GA levels in two Arabidopsis mutants in which GA2ox7 and GA2ox8 were activation-tagged, and ectopic overexpression of these two genes in transgenic tobacco led to dwarf phenotype (Schomburg et al., 2003). These studies demonstrated that GA2oxs are responsible for reducing the endogenous level of biologically active GAs in plants. The class C20 GA2oxs, regulating early steps in the GA biosynthesis pathway, have also been shown to control photoperiods in dicots. In long-day (LD) rosette plants, such as spinach, LD-induced stem elongation and flowering are dependent on GA-regulated processes. In short-day (SD) plants, deactivation of GA₅₃ to GA₉₇ prevails, while in LD plants, conversion of GA₅₃ to the bioactive GA₂₀ and GA₁ is favored (Lee and Zeevaart, 2005).

The functions of four rice GA2oxs have been previously studied (Sakamoto, et al., 2001, 2004; Sakai et al., 2003). There is a need to identify and study the physiological functions of additional GA2oxs.

SUMMARY OF THE INVENTION

Ten (10) putative GA2ox genes have now been identified from the sequence analysis of the rice genome. Differential expression of the GA2ox genes was found to correlate with various developmental processes during rice growth, such as flower development, seed germination and tiller growth.

In one general aspect, the present invention relates to an isolated nucleic acid comprising a nucleotide sequence that encodes a polypeptide selected from the group consisting of:

(a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6;

(b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8;

(c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; and

(d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.

In another general aspect, the present invention relates to an isolated polypeptide comprising an amino acid sequence selected from the group consisting of:

(a) an amino acid sequence that is at least about 80% identical to SEQ ID NO:6;

(b) an amino acid sequence that is at least about 80% identical to SEQ ID NO:8;

(c) an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; and

(d) an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.

Another general aspect of the present invention relates to an isolated nucleic acid comprising a nucleotide sequence that encodes a mutant class C20 gibberellin 2-oxidase protein (GA2ox), the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, wherein the domain III comprises an amino acid sequence of SEQ ID NO:17.

Another general aspect of the present invention relates to an isolated polypeptide comprising a mutant class C20 gibberellin 2-oxidase (GA2ox), the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, wherein the domain III comprises the amino acid sequence of SEQ ID NO:17.

Other general aspects of the present invention relate to an expression vector and a recombinant cell comprising a nucleic acid according to an embodiment of the present invention.

In another general aspect, the present invention relates to a transgenic plant comprising a transgene, wherein the transgene encodes a polypeptide selected from the group consisting of:

(a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:2;

(b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:4;

(c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6;

(d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8;

(e) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12;

(f) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16; and

(g) a mutant class C20 GA2ox, the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, and the domain III comprising the amino acid sequence of SEQ ID NO:17.

The present invention also relates to a propagation material obtained from the transgenic plant of the present invention, wherein the propagation material contains the transgene.

In another general aspect, the present invention relates to a method of producing a transgenic plant according to embodiments of the present invention, comprising:

(a) transforming a plant cell with a nucleic acid molecule comprising a transgene according to an embodiment of the present invention to obtain a recombinant plant cell; and

(b) growing the recombinant plant cell obtained in (a) to generate a transgenic plant.

Another general aspect of the present invention relates to a method of inhibiting plant growth, comprising:

(a) transforming a plant cell with a nucleic acid molecule comprising a transgene according to an embodiment of the present invention to obtain a recombinant plant cell that expresses a recombinant polypeptide; and

(b) growing the recombinant plant cell obtained in (a) to generate a transgenic plant;

wherein the recombinant polypeptide is expressed in the transgenic plant at a level sufficient to inhibit growth of the transgenic plant.

Another general aspect of the present invention relates to a method of obtaining a semi-dwarf transgenic plant, comprising:

(a) providing a transgenic plant according to an embodiment of the present invention or a propagation material thereof;

(b) growing the transgenic plant or the propagation material thereof, so that a recombinant polypeptide is expressed in the transgenic plant at a level sufficient to inhibit growth of the transgenic plant; and

(c) applying to the transgenic plant or the propagation material thereof a composition comprising at least one bioactive GA compound, so that the transgenic plant or propagation material thereof produces the semi-dwarf transgenic plant.

Another general aspect of the present invention relates to a method of inhibiting stem elongation and promoting tiller growth in a plant, comprising administering to the plant a compound that increases the expression of a gene encoding a polypeptide or a compound that increases the enzymatic activity of the polypeptide in the plant, wherein the polypeptide is selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:2;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:4;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (e) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or at least about 80%         identical to SEQ ID NO:12; and     -   (f) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or at least about 80%         identical to SEQ ID NO:16.

Another general aspect of the present invention relates to a method of identifying a compound that inhibits stem elongation and promotes tiller growth in a plant, comprising identifying a compound that increases the expression of a gene encoding a polypeptide or a compound that increases the enzymatic activity of the polypeptide in the plant, wherein the polypeptide is selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:2;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:4;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (e) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or at least about 80%         identical to SEQ ID NO:12; and     -   (f) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or at least about 80%         identical to SEQ ID NO:16.

Other aspects, features and advantages of the invention will be apparent from the following disclosure, including the detailed description of the invention and its preferred embodiments and the appended claims.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

The foregoing summary, as well as the following detailed description of the invention, will be better understood when read in conjunction with the appended drawing. For the purpose of illustrating the invention, there is shown in the drawing embodiments of the invention. It should be understood, however, that the invention is not limited to the precise arrangements and instrumentalities shown.

In the drawings:

FIGS. 1A-1C illustrate the rice GA2ox family: FIG. 1A shows chromosome locations of GA2oxs as determined by the NCBI map viewer program (www.ncbi.nlm.nih.gov/mapview/); FIG. 1B shows the phylogenetic tree based on the comparison of deduced amino acid sequences of rice GA2oxs; FIG. 1C shows the phylogenetic tree based on the comparison of amino acid sequences of 29 GA2oxs from 9 plant species (Table 3); wherein the plant species are: At, Arabidopsis thaliana; Cm, Cucurbita maxima; Ls, Lactuca sativa; Nt, Nicotiana sylvestris; Pc, Phaseolus coccineus; Po, Populus alba x P. tremuloides; Ps, Pisum sativum; and So, Spinacia oleracea; wherein GA2oxs with three unique highly conserved domains are enclosed in squares;

FIGS. 2A-2C illustrate differential expression of GA2oxs that correlated with flower and tiller development: FIG. 2A shows various developmental phases during the life cycle of rice; FIG. 2B shows temporal expression patterns of GA2oxs in rice, wherein the 18S rRNA gene (rRNA) was used as a control; FIG. 2C shows tiller development during the life cycle of rice, wherein a total of 8 plants were used for counting tiller number and error bars indicate the SE (standard errors) of the mean at each time point, and DAI means days after imbibition;

FIGS. 3A and 3B illustrate decrease in GA2ox6 expression that correlated with seed germination: FIG. 3A shows that germination rate of rice seeds reached 100% at 2 DAI; FIG. 3B shows expression patterns of GA2oxs in rice seeds between 0˜5 DAI, wherein total RNAs were isolated from embryos at each time point and analyzed by RT-PCR, and wherein the 18S rRNA gene (rRNA) was used as a control;

FIGS. 4A-4D illustrate four GA2ox mutants identified from the TRIM mutant library: FIG. 4A shows the severely dwarf mutant M77777, designated as GA2ox3_(ACT), which carries a T-DNA insertion at a position 587 bp upstream of the translation start codon of GA2ox3, wherein accumulation of GA2ox3 mRNA in this mutant was significantly enhanced in the heterozygous (T/W) mutant as analyzed by RT-PCR analysis; FIG. 4B shows the semi-dwarf mutant M27337, designated as GA2ox5 Δ335-341_(ACT), which carries a T-DNA insertion in the coding region, at a position 23 bp upstream of the translation stop codon of GA2ox5, wherein accumulation of the truncated GA2ox5 mRNA was significantly enhanced by T-DNA activation tagging in both heterozygous and homozygous (T/T) mutants; FIG. 1C shows the severely dwarf mutant M47191, designated as GA2ox6_(ACT), which carries a T-DNA insertion at a position 2.1 kb upstream of the translation start codon of GA2ox6, wherein accumulation of GA2ox6 mRNA was significantly enhanced by T-DNA activation tagging in both heterozygous and homozygous mutants; and FIG. 4D shows the semi-dwarf mutant M58817, designated as GA2ox9_(ACT), which carries a T-DNA insertion at a position 2.4 kb upstream of the translation start codon of GA2ox9, wherein accumulation of GA2ox9 mRNA was significantly enhanced by T-DNA activation tagging in the homozygous mutant; wherein in the diagram, an asterisk indicates translation start codon, filled box indicates exon, triangle indicates T-DNA, arrowheads indicate position of primers used for RT-PCR analysis, and scale bar represents DNA length for each gene, and the open box in the triangle indicates the position of the CaMV35S enhancers (next to the left border of T-DNA);

FIGS. 5A-5C illustrate that activation of GA2oxs expression had different effect on seed germination and seedling growth: FIG. 5A shows morphology of T1 seedlings at 18 DAI; FIG. 5B shows that seedling heights of GA2ox5 Δ335-341_(ACT) and GA2ox9_(ACT) mutants were slightly shorter while seedlings of GA2ox6_(ACT) were severely shorter than the wild type, wherein heights of 8 plants in each line were measured and error bars indicate the SE of the mean at each time point; FIG. 5C shows that as compared with the wild type, germination rate was normal for GA2ox9_(ACT) mutant, slightly delayed for GA2ox5 Δ335-341_(ACT) mutant, and significantly delayed for GA2ox6_(ACT) mutant; wherein germination rates of 154, 20, 156, 49 seeds for TNG67, GA2ox5 Δ335-341_(ACT), GA2ox6_(ACT), and GA2ox9_(ACT), respectively, were determined at each time point, and + and − indicate the presence and absence, respectively;

FIGS. 6A-6D illustrate that overexpression of GA2ox5 and GA2ox6 recapitulated the dwarf phenotypes in transgenic rice and tobacco: FIGS. 6A and 6B show that expression of Ubi::GA2ox5 and Ubi::GA2ox6, respectively, resulted in dwarfism in transgenic rice as compared with control rice transformed with vector pCAMBIA1301 only (CK); FIGS. 6C and 6D show that expression of Ubi::GA2ox5 and Ubi::GA2ox6, respectively, resulted in different degrees of dwarfism in transgenic tobacco as compared with control tobacco transformed with vector only (CK); wherein photographs were taken at the heading stage (upper panel) and 18 days (lower panel) after sowing of seeds;

FIGS. 7A-7C show that overexpression of GA2ox6 reduced GA levels in rice mutant in which only shoot but not root growth was affected: FIG. 7A shows that treatment with GA₃ (5 μM) promoted germination and seedling growth of GA2ox6_(ACT) mutant (photo taken at 6 DAI); FIG. 7B shows that overexpression of GA2ox6 in rice mutants reduced shoot but not root growth, wherein treatment with GA₃ (5 μM) recovered plant height of the GA2ox⁶ _(ACT) mutant and root growth of both wild type and mutant, and a total of 8 plants were used for measuring plant height and root length and error bars indicate the SE of the mean; FIG. 7C illustrates that accumulation of GA2ox6 mRNA in leaves and roots of wild type and mutant seedlings (at 18 DAI) was not altered by GA₃ treatment, wherein the 18S rRNA gene (rRNA) was used as a control, and WT stands for wild type;

FIGS. 8A-8F illustrate that overexpression of GA2ox5 and GA2ox6 promoted early tiller and adventitious root growth and affects root architecture: FIG. 8A shows that swelling on the embryo surface adjacent to the base of the first seedling/tiller (1T) was observed in the GA2ox6_(ACT) mutant and Ubi::OsGA2ox5 and Ubi::OsGA2ox6 transgenic rice (panels 2-4) and not in the wild type (panel 1) (photos taken at 3 DAI); FIG. 8 B shows that a second tiller (2T) grew out from the swollen embryo surface of mutant and transgenic rice (photo taken at 9 DAI); FIG. 8C shows that three tillers formed in some seedlings of mutant and transgenic rice (photo taken at 15 DAI); FIG. 8D shows that each tiller grew out of its own coleoptile and all new tillers in the mutant and transgenic rice had their own adventitious roots (photo taken at 21 DAI), wherein panel 2 is a higher magnification of the boxed area in panel 1 that reveals coleoptiles (1C and 2C, respectively) and adventitious roots (1R and 2R, respectively) of the first and second tillers; FIG. 8E shows dwarfism and early tillering of seedlings of mutant and transgenic rice as compared with the wild type (photo taken at 12 DAI), wherein panel 2 is a higher magnification of the boxed area in panel 1 that reveals first and second tillers; FIG. 8F shows that mutant and transgenic roots became highly curled and zigzag (panel 2) as compared with the wild type (panel 1), wherein photos were taken at 15 DAI from the bottom of agar plates for better visualization of root growth and WT stands for wild type.

FIGS. 9A-C show that overexpression of GA2ox5 and GA2ox6 decreased plant heights, but increased tiller numbers and root numbers: FIG. 9A shows plant heights of various plants; FIG. 9B shows tiller of various plants; FIG. 9C shows root numbers of various plants; wherein mutant or transgenic rice seeds germinated on MS agar medium for 18 DAI, ten plants in each line were averaged and error bars indicate the SE of the mean, and wherein WT stands for wild type;

FIGS. 10A and 10B illustrate that mutations in domain III affected the activity of GA2ox5 and GA2ox6: FIG. 10A shows design of constructs encoding the full-length and domain III-truncated GA2ox5 and GA2ox6, wherein boxes indicate positions of three highly conserved amino acid domains, and the last amino acid residue was shown at the C-terminus of deduced polypeptides; FIG. 10B shows the comparison of morphology among transgenic rice overexpressing full-length and domain-III-truncated GA2ox5 and GA2ox6 and vector pCAMBIA1301 only (CK);

FIG. 11 illustrates amino acid sequence alignment of rice GA2oxs, including OsGA2ox5 (SEQ ID NO: 2), OsGA2ox6 (SEQ ID NO:4) and OsGA2ox9 (SEQ ID NO: 10); Arabidopsis GA2oxs, including AtGA2ox7 (SEQ ID NO: 24) and AtGA2ox8 (SEQ ID NO:25); and spinach GA2ox, including SoGA2ox3 (SEQ ID NO: 26), using the Vector NTI 6.0 software (InforMax, Inc.), wherein these GA2oxs contain three highly conserved domains (underlined) that are absent in other GA2oxs (Lee and Zeevaart, 2005); and

FIGS. 12A and 12B show dwarfism of Ubi::GA2ox6 transgenic rice that is partially rescued by GA₃: Wild type (WT) and Ubi::GA2ox6 transgenic rice grown in pot soil were treated with (+) or without (−) 10 μM GA₃ at a 12-day interval for 5 weeks; the height of WT plant was not altered, while that of transgenic plant was enhanced, by GA₃ treatment; FIG. 12A shows morphology of plants, and FIG. 12B shows growth curve of plants; the height of transgenic plants increased linearly during first 10 days, tapered off afterward, and finally only reached 63% of the WT; arrows indicate dates for GA₃ treatment.

DETAILED DESCRIPTION OF THE INVENTION

It will be appreciated by those skilled in the art that changes could be made to the embodiments described above without departing from the broad inventive concept thereof. It is understood, therefore, that this invention is not limited to the particular embodiments disclosed, but it is intended to cover modifications within the spirit and scope of the present invention as defined by the appended claims.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention pertains. Otherwise, certain terms used herein have the meanings as set in the specification. All patents, published patent applications and publications cited herein are incorporated by reference as if set forth fully herein. It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.

As used herein, the term “gene” refers to a segment of DNA involved in producing a functional RNA. A gene includes the coding region, non-coding regions preceding (“5′UTR”) and following (“3′UTR”) the coding region, alone or in combination. The functional RNA can be an mRNA that is translated into a peptide, polypeptide, or protein. The functional RNA can also be a non-coding RNA that is not translated into a protein species, but has a physiological function otherwise. Examples of the non-coding RNA include, but are not limited to, a transfer RNA (tRNA), a ribosomal RNA (rRNA), a micro RNA, a ribozyme, etc. A “gene” can include intervening non-coding sequences (“introns”) between individual coding segments (“exons”). A “coding region” or “coding sequence” refers to the portion of a gene that is transcribed into an mRNA, which is translated into a polypeptide and the start and stop signals for the translation of the corresponding polypeptide via triplet-base codons. A “coding region” or “coding sequence” also refers to the portion of a gene that is transcribed into a non-coding but functional RNA.

As used herein, a “promoter” refers to a portion of a gene that provides a control point for regulated gene transcription. A promoter can include a binding site for RNA polymerase. A promoter can also include one or more binding sites for one or more transcription factors. A promoter is often upstream of (“5′ to”) the transcription initiation site of a gene. A promoter is typically adjacent to the transcriptional start site of the gene. However, a promoter can also be located at a distance from the transcriptional start site of the gene.

As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site, where transcription of RNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from −1, for example −100 is a position 100 base pairs upstream). Conventional notation is used herein to describe polynucleotide sequences. The left-hand end of a single-stranded polynucleotide sequence is the 5′-end, and the left-hand direction of a single-stranded polynucleotide sequence is referred to as the 5′-direction. The left-hand end of a double-stranded polynucleotide sequence is the 5′-end of the plus strand, which is depicted as the top strand of the double strands, and the right-hand end of the double-stranded polynucleotide sequence is the 5′-end of the minus strand, which is depicted as the bottom strand of the double strands. The direction of 5′ to 3′ addition of nucleotides to nascent RNA transcripts is referred to as the transcription direction. A DNA strand having the same sequence as an mRNA is referred to as the “coding strand.” Sequence on a DNA strand which is located 5′ to a reference point on the DNA is referred to as “upstream sequence”; sequence on a DNA strand which is 3′ to a reference point on the DNA is referred to as “downstream sequence.”

As used herein, “operably linked” refers to a functional relationship between two nucleotide sequences. A single-stranded or double-stranded nucleic acid moiety comprises the two nucleotide sequences arranged within the nucleic acid moiety in such a manner that at least one of the two nucleotide sequences is able to exert a physiological effect by which it is characterized upon the other. By way of example, a promoter sequence that controls transcription of a coding sequence is operably linked to that coding sequence. Operably linked nucleic acid sequences can be contiguous, typical of many promoter sequences, or non-contiguous, in the case of, for example, nucleic acid sequences that encode repressor proteins. Within a recombinant expression vector, “operably linked” is intended to mean that the coding sequence of interest is linked to the regulatory sequence(s) in a manner that allows for expression of the coding sequence, e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell.

“Sequence” means the linear order in which monomers occur in a polymer, for example, the order of amino acids in a polypeptide or the order of nucleotides in a polynucleotide.

As used herein, the term “nucleotide sequence”, “nucleic acid” or “polynucleotide” refers to the arrangement of either deoxyribonucleotide or ribonucleotide residues in a polymer in either single- or double-stranded form. Nucleic acid sequences can be composed of natural nucleotides of the following bases: T, A, C, G, and U, and/or synthetic analogs of the natural nucleotides. In the context of the present invention, adenosine is abbreviated as “A”, cytidine is abbreviated as “C”, guanosine is abbreviated as “G”, thymidine is abbreviated as “T”, and uridine is abbreviated as “U”.

As used herein, an “isolated” nucleic acid molecule is one that is substantially separated from at least one of the other nucleic acid molecules present in the natural source of the nucleic acid, or is substantially free of at least one of the chemical precursors or other chemicals when the nucleic acid molecule is chemically synthesized. An “isolated” nucleic acid molecule can also be, for example, a nucleic acid molecule that is substantially free of at least one of the nucleotide sequences that naturally flank the nucleic acid molecule at its 5′ and 3′ ends in the genomic DNA of the organism from which the nucleic acid is derived. A nucleic acid molecule is “substantially separated from” or “substantially free of” other nucleic acid molecule(s) or other chemical(s) in preparations of the nucleic acid molecule when there is less than about 30%, 20%, 10%, or 5% or less, and preferably less than 1%, (by dry weight) of the other nucleic acid molecule(s) or the other chemical(s) (also referred to herein as a “contaminating nucleic acid molecule” or a “contaminating chemical”).

Isolated nucleic acid molecules include, without limitation, separate nucleic acid molecules (e.g., cDNA or genomic DNA fragments produced by PCR or restriction endonuclease treatment) independent of other sequences, as well as nucleic acid molecules that are incorporated into a vector, an autonomously replicating plasmid, a virus (e.g., a retrovirus, adenovirus, or herpes virus), or into the genomic DNA of a prokaryote or eukaryote. In addition, an isolated nucleic acid molecule can include a nucleic acid molecule that is part of a hybrid or fusion nucleic acid molecule. An isolated nucleic acid molecule can be a nucleic acid sequence that is: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) synthesized by, for example, chemical synthesis; (iii) recombinantly produced by cloning; or (iv) purified, as by cleavage and electrophoretic or chromatographic separation.

A polynucleotide can have a single strand or parallel and anti-parallel strands. Thus, a polynucleotide may be a single-stranded or a double-stranded nucleic acid. Unless otherwise indicated, a polynucleotide is not defined by length and thus includes very large nucleic acids, as well as short ones, such as an oligonucleotide.

“Sequence identity or similarity”, as known in the art, is the relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. As used herein, “identity”, in the context of the relationship between two or more nucleic acid sequences or two or more polypeptide sequences, refers to the percentage of nucleotide or amino acid residues, respectively, that are the same when the sequences are optimally aligned and analyzed. For purposes of comparing a queried sequence against, for example, the amino acid sequence SEQ ID NO: 6, the queried sequence is optimally aligned with SEQ ID NO: 6 and the best local alignment over the entire length of SEQ ID NO: 6 is obtained.

Analysis can be carried out manually or using sequence comparison algorithms. For sequence comparison, typically one sequence acts as a reference sequence, to which a queried sequence is compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, sub-sequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.

Optimal alignment of sequences for comparison can be conducted, for example, by using the homology alignment algorithm of Needleman & Wunsch, J Mol. Biol., 48:443 (1970). Software for performing Needleman & Wunsch analyses is publicly available through the Institut Pasteur (France) Biological Software website: http://bioweb.pasteur.fr/seqanal/interfaces/needle.html. The NEEDLE program uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length. The identity is calculated along with the percentage of identical matches between the two sequences over the reported aligned region, including any gaps in the length. Similarity scores are also provided wherein the similarity is calculated as the percentage of matches between the two sequences over the reported aligned region, including any gaps in the length. Standard comparisons utilize the EBLOSUM62 matrix for protein sequences and the EDNAFULL matrix for nucleotide sequences. The gap open penalty is the score taken away when a gap is created; the default setting using the gap open penalty is 10.0. For gap extension, a penalty is added to the standard gap penalty for each base or residue in the gap; the default setting is 0.5.

Hybridization can also be used as a test to indicate that two polynucleotides are substantially identical to each other. Polynucleotides that share a high degree of identity will hybridize to each other under stringent hybridization conditions. “Stringent hybridization conditions” has the meaning known in the art, as described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1989). An exemplary stringent hybridization condition comprises hybridization in a medium comprising 4-6× sodium chloride/sodium citrate (SSC) at about 45-65° C., followed by one or more washes in 0.2×SSC and 0.1% SDS at 50-65° C., depending upon the length over which the hybridizing polynucleotides share complementarity or percent of identity.

As used herein, the terms “polypeptide” and “protein” are used herein interchangeably to refer to amino acid chains in which the amino acid residues are linked by peptide bonds or modified peptide bonds. The amino acid chains can be of any length of greater than two amino acids. Unless otherwise specified, the terms “polypeptide” and “protein” also encompass various modified forms thereof. Such modified forms may be naturally occurring modified forms or chemically modified forms. Examples of modified forms include, but are not limited to, glycosylated forms, phosphorylated forms, myristoylated forms, palmitoylated forms, ribosylated forms, acetylated forms, ubiquitinated forms, etc. Modifications also include intra-molecular crosslinking and covalent attachment to various moieties such as lipids, flavin, biotin, polyethylene glycol or derivatives thereof, etc. In addition, modifications may also include cyclization, branching and cross-linking. Further, amino acids other than the conventional twenty amino acids encoded by the codons of genes may also be included in a polypeptide.

An “isolated protein” or “isolated polypeptide” is one that is substantially separated from at least one of the other proteins present in the natural source of the protein, or is substantially free of at least one of the chemical precursors or other chemicals when the protein is chemically synthesized. A protein is “substantially separated from” or “substantially free of” other protein(s) or other chemical(s) in preparations of the protein when there is less than about 30%, 20%, 10%, or 5% or less, and preferably less than 1% (by dry weight) of the other protein(s) or the other chemical(s) (also referred to herein as a “contaminating protein” or a “contaminating chemical”).

Isolated proteins can have several different physical forms. The isolated protein can exist as a full-length nascent or unprocessed polypeptide, or as a partially processed polypeptide or as a combination of processed polypeptides. The full-length nascent polypeptide can be postranslationally modified by specific proteolytic cleavage events that result in the formation of fragments of the full-length nascent polypeptide. A fragment, or physical association of fragments can have the biological activity associated with the full-length polypeptide; however, the degree of biological activity associated with individual fragments can vary.

An isolated polypeptide or isolated protein can be a non-naturally occurring polypeptide. For example, an isolated polypeptide can be a “hybrid polypeptide.” An isolated polypeptide can also be a polypeptide derived from a naturally occurring polypeptide by additions or deletions or substitutions of amino acids. An isolated polypeptide can also be a “purified polypeptide” which is used herein to mean a specified polypeptide in a substantially homogeneous preparation substantially free of other cellular components, other polypeptides, viral materials, or culture medium, or when the polypeptide is chemically synthesized, chemical precursors or by-products associated with the chemical synthesis. A “purified polypeptide” can be obtained from natural or recombinant host cells by standard purification techniques, or by chemical synthesis, as will be apparent to skilled artisans.

As used herein, “recombinant” refers to a polynucleotide, a polypeptide encoded by a polynucleotide, a cell, a viral particle or an organism that has been modified using molecular biology techniques to something other than its natural state.

As used herein, a “recombinant cell” or “recombinant host cell” is a cell that has had introduced into it a recombinant polynucleotide sequence. For example, recombinant cells can contain at least one nucleotide sequence that is not found within the native (non-recombinant) form of the cell or can express native genes that are otherwise abnormally expressed, under-expressed, or not expressed at all. Recombinant cells can also contain genes found in the native form of the cell wherein the genes are modified and re-introduced into the cell by artificial means. The term also encompasses cells that contain an endogenous nucleic acid that has been modified without removing the nucleic acid from the cell; such modifications include those obtained, for example, by gene replacement, and site-specific mutation. The term encompasses cells that contain the recombinant polynucleotide sequence either on a vector, such as an expression vector, or integrated into a cell chromosome.

Recombinant DNA sequence can be introduced into host cells using any suitable method including, for example, electroporation, calcium phosphate precipitation, microinjection, transformation, biolistics and viral infection. Recombinant DNA may or may not be integrated (covalently linked) into chromosomal DNA making up the genome of the cell. For example, the recombinant DNA can be maintained on an episomal element, such as a plasmid. Alternatively, with respect to a stably transformed or transfected cell, the recombinant DNA has become integrated into the chromosome so that it is inherited by daughter cells through chromosome replication. This stability is demonstrated by the ability of the stably transformed or transfected cell to establish cell lines or clones comprised of a population of daughter cells containing the exogenous DNA. It is further understood that the term “recombinant host cell” refers not only to the particular subject cell, but also to the progeny or potential progeny of such a cell. Because certain modifications can occur in succeeding generations due to either mutation or environmental influences, and in such circumstances, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

As used herein, the term “transgenic plant” or “transgenic line” refers to a plant that contains a recombinant nucleotide sequence that encodes a gene, i.e., a transgene. The transgenic plant can be grown or derived from a recombinant cell. A transgenic plant includes progeny, offspring, clone, breeding material or propagation material, such as seeds, thereof that comprises the transgene.

As used herein, the term “semi-dwarf transgenic plant” means a transgenic plant having the phenotypic trait of a reduced height of the stem or size that is about 50% to 90% of a non-transgenic plant of the same genetic background while being grown under the same conditions. For example, the semi-dwarf transgenic plant can have a height of the stem that is about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% of a non-transgenic plant of the same genetic background while being grown under the same conditions.

As used herein, the term “dwarf transgenic plant” means a transgenic plant having the phenotypic trait of a reduced height of the stem or size that is about 20% to 50% of a non-transgenic plant of the same genetic background while being grown under the same conditions. For example, the dwarf transgenic plant can have a height of the stem that is about 20%, 25%, 30%, 35%, 40%, 45%, or 50% of a non-transgenic plant of the same genetic background while being grown under the same conditions.

As used herein, the term “severely dwarf transgenic plant” means a transgenic plant having the phenotypic trait of a reduced height of the stem or size that is less than about 20% of a non-transgenic plant of the same genetic background while being grown under the same conditions.

As used herein, the term “cereal plant” or “cereal crop” refers to a species of true grasses, i.e., Poaceae or Gramineae family in the Class Liliopsida of the flowering plants, or a species of pseudocereals, that is cultivated for its edible grains or seeds. Cereal plants are staple crops grown in greater quantities and provide more energy worldwide than any other type of crop. Cereal grains are a rich source of carbohydrate. Examples of cereal plants include, but are not limited to, plants of maize, rice, wheat, barley, sorghum, millets, oats, rye, triticale, buckwheat, fonio, quinoa, etc.

As used herein, an “expression vector” refers to a nucleic acid molecule that is used to recombinantly express a gene in a target cell. A heterologous or isolated nucleic acid encoding a gene of interest can be or is inserted into an expression vector. The expression vector with the heterologous or isolated nucleic acid can be or is introduced into a host cell. Once the expression vector is inside the cell, the gene product encoded by the heterologous or isolated nucleic acid is produced by the transcription and translation machinery of the host cell. An expression vector typically has for example, an origin of replication sequence allowing replication of the expression vector in the host cell, multiple cloning sites allowing insertion of the heterologous or isolated nucleic acid, a promoter allowing transcription of a gene of interest in the host cell, a heterologous or isolated nucleic acid encoding the gene of interest, a selectable marker gene that encodes a gene product allowing selection of the host cell containing the expression vector from those that do not. The properties, construction and use of expression vectors in the present invention will be readily apparent to those of skill in view of the present disclosure. For example, the expression vector according to embodiments of the present invention can be a plasmid that is replicable in an agrobacterium and contains a stress-inducible promoter operably linked to the coding sequence of a stress-resistant gene.

The terms “gibberellin 2-oxidase protein,” “GA 2-oxidase,” and “GA2ox”, as used herein interchangeably, all refer to a 2-oxoglutarate-dependent dioxygenase (2-ODD) that catalyzes the inactivation of biologically active gibberellin (GA) and/or its precursors, thus reducing the endogenous levels of bioactive GAs.

A “GA2ox” can be a class C19 GA2ox, that catalyzes 2β-hydroxylation of the C-2 of biologically active C₁₉-GAs (GA₁ and GA₄) or C₁₉-GA precursors (GA₂₀ and GA₉) to produce biologically inactive GAs (GA₈, GA₃₄, GA₂₉, and GA₅₁, respectively). Examples of C19 GA2ox include, but are not limited to, rice GA2oxs 1-4, GA2ox7, GA2ox8 and GA2ox10.

A “GA2ox” can also be a class C20 GA2ox, that catalyzes 2β-hydroxylation of C₂₀-GA precursors but not C₁₉-GAs. The 2β-hydroxylation of C₂₀-GA precursors, e.g., converting GA₁₂ and GA₅₃ to GA₁₁₀ and GA₉₇, respectively, renders them unable to be converted to active GAs and thus decreases active GA levels. The class C20 GA2oxs contain three unique and conserved amino acid domains that are absent in the class C19 GA2oxs (Lee and Zeevaart, 2005). Examples of C20 GA2ox include, but are not limited to, Arabidopsis GA2ox7 and GA2ox8, spinach GA2ox3, and rice GA2ox5, GA2ox6 and GA2ox9.

As used herein, the term “bioactive gibberellin compound” and “bioactive GA compound”, as used herein interchangeably, all refer to a gibberellin or a derivative thereof that regulates growth and influences various developmental processes of a plant. Depending on the type of gibberellin present as well as the species of plant, the physiological effects of a bioactive GA include, but are not limited to, one or more selected from the group consisting of stimulating stem elongation, stimulating bolting/flowering, breaking seed dormancy, stimulating germination, inducing sex expression, enzyme induction, causing parthenocarpic (seedless) fruit development, and delaying senescence in leaves and fruits. Examples of bioactive GA compound include, but are not limited to, GA₁, GA₃, GA₄ and GA₇.

In the present study, 10 putative rice GA2ox genes were identified, and differential expression of nine of them correlated with various developmental processes during rice growth, such as flower development, seed germination and tiller growth. Differential expression and/or biological activities of GA2oxs can give rise to some beneficial phenotypes in rice, including semi-dwarfism, increased root system and higher tiller numbers that may favor grain yield. In addition to some known effects caused by overexpression of GA2oxs, the early and increased growth of tiller and adventitious root and altered root architecture further suggest the pleiotropic role of GA2oxs in controlling rice growth and architecture.

GA2ox5, GA2ox6 and GA2ox9 were three genes encoding class C20 GA2oxs in rice, and their functions were further investigated using T-DNA activation tagged rice mutants and transgenic ectopic overexpression approaches. Mutants or transgenic rice recombinantly expressing class C20 GA2oxs, under the control of their native promoters or a constitutive promoter, exhibited a broad range of mutant phenotypes. Mutations in the conserved domain III were found to affect the physiological activity of class C20 GA2oxs, suggesting domain III is important for the proper biological activity of class C20 GA2oxs. Overexpression of GA2ox5 with partially functional domain III significantly alleviated the mutant phenotype.

Embodiments of the present invention demonstrate that improvement of plant architecture can be achieved by overexpression of certain wild-type or mutant GA2oxs under the control of various promoters, such as the native, constitutive, or inducible promoters.

Accordingly, one general aspect of the present invention relates to an isolated nucleic acid, comprising a nucleotide sequence that encodes a polypeptide selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or at least about 80%         identical to SEQ ID NO:12; and     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or at least about 80%         identical to SEQ ID NO: 16.

The invention encompasses any isolated nucleic acid encoding an amino acid sequence that is at least about 80% identical to SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 or SEQ ID NO:16. In embodiments of the present invention, the nucleic acid encodes an amino acid sequence that is 80%, 85%, 90%, 95%, or 100% identical to SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 or SEQ ID NO:16. In particular embodiments of the present invention, the nucleic acid can be genomic DNAs, cDNAs, and chemically synthesized DNAs.

Due to the degeneracy of the genetic code, more than one codon may be used to encode a particular amino acid, and therefore, an amino acid sequence (for example, SEQ ID NO: 6) can be encoded by any one of a plurality of nucleic acid sequences. Isolated nucleic acid includes sequences wherein one or more codons in the sequence are replaced by codons of a different sequence but that code for the same amino acid residue are herein referred to as “conservative codon substitutions”.

In one embodiment, the invention encompasses nucleic acid sequences that have one or more than one conservative codon substitutions. One of skill in the art would be able to determine a particular nucleic acid sequence having one or more than one conservative codon substitutions and encoding the above amino acid sequence, based on the sequence information provided herein. Conservative codon substitutions can be made in the nucleic acid sequence encoding the polypeptide, for example, the codons TTT and TTC (collectively referred to as TTT/C) can encode a Phe (phenylalanine) residue; other exemplary codon substitutions include, but are not limited to: TTA/G and CTT/C/A/G: Leu; ATT/C: Ile; ATG: Met; GTT/C/A/G: Val; TCT/C/A/G: Ser; CCT/C/A/G: Pro; ACT/C/A/G: Thr; GCT/C/A/G: Ala; TAT/C: Tyr; CAT/C: His; CAA/G: Gln; AAT/C: Asn; AAA/G: Lys; GAT/C: Asp; GAA/G Glu; TGT/C: Cys; CGT/C/A/G: Arg; AGT/C: Ser; AGA/G; Arg; GGT/C/A/G:Gly. Conservative codon substitutions can be made at any position in the nucleic acid sequence that encodes the recited amino acid sequence.

In an embodiment of the present invention, the isolated nucleic acid comprises a nucleotide sequence that encodes a polypeptide selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16.

In another embodiment of the present invention, the isolated nucleic acid comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13 and SEQ ID NO:15.

A nucleic acid according to embodiments of the present invention can be readily designed, synthesized and isolated using methods known in the art, in view of the present disclosure. For example, a genomic DNA or cDNA can be prepared according to conventional methods known to those skilled in the art in view of the present disclosure. In one embodiment, genomic DNA can be prepared as follows: (1) extract a genomic DNA from rice cultivars having a DNA encoding a protein with a GA2-oxidation activity; (2) construct a genomic library (utilizing a vector such as a plasmid, phage, cosmid, BAC, or PAC); (3) spread the library; and (4) conduct colony hybridization or plaque hybridization using a probe prepared based on a DNA encoding a polypeptide that is at least about 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16. In another embodiment, a genomic DNA can be prepared via PCR using primers specific for a DNA encoding a polypeptide that is at least about 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16. cDNA can be prepared as follows: (1) synthesize cDNAs based on mRNAs extracted from rice cultivars having a DNA encoding a protein with a GA2-oxidation activity; (2) prepare a cDNA library by inserting the synthesized cDNA into a vector such as λZAP; (3) spread the cDNA library; and (4) conduct colony hybridization or plaque hybridization as described above. Alternatively, cDNA can also be prepared by RT-PCR. The DNA can be isolated by gel electrophoresis.

A nucleic acid according to embodiment of the present invention can be used to express a polypeptide of the present invention. The nucleic acid can also be used to produce an expression vector, a recombinant cell or a transgenic plant. Preferably, the polypeptide, expression vector, recombinant cell and transgenic plant can be used to regulate plant development, e.g., to suppress plant growth resulting in a semi-dwarf transgenic plant.

In another general aspect, the present invention relates to an isolated polypeptide comprising an amino acid sequence selected from the group consisting of:

-   -   (a) an amino acid sequence that is at least about 80% identical         to SEQ ID NO:6;     -   (b) an amino acid sequence that is at least about 80% identical         to SEQ ID NO:8;     -   (c) an amino acid sequence that is at least about 80% identical         to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12;         and     -   (d) an amino acid sequence that is at least about 80% identical         to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.

The invention encompasses any isolated polypeptide comprising an amino acid sequence that is at least about 80% identical to SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 or SEQ ID NO:16. In embodiments of the present invention, the polypeptide comprises an amino acid sequence that is 80%, 85%, 90%, 95%, or 100% identical to SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 or SEQ ID NO:16. Preferably, the polypeptide has GA2ox biological activity.

The polypeptide according to embodiment of the present invention can have additional amino acid residues. In some embodiments, the additional amino acids are present at the amino terminus, the carboxyl terminus, within the polypeptide sequence or combinations of these locations. Polypeptides having these types of additional amino acid sequences can be referred to as “fusion proteins”. In some cases, it may be more appropriate to refer to them otherwise as “chimeric” or “tagged” proteins, or the like, depending on the nature of the additional amino acid sequences. Nonetheless, one will be able to discern a polypeptide having additional amino acid sequences given the sequence information provided herein. The additional amino acid residues can be short, for example, from one to about 20 additional amino acid residues, or longer, for example, greater than about 20 additional amino acid residues. The additional amino acid residues can serve one or more functions or purposes including, for example, serving as epitopes for protein (e.g., antibody) or small molecule binding; serving as tags for intracellular and extracellular trafficking; providing additional enzymatic or other activity; or providing a detectable signal.

For example, the fusion protein can include additional amino acid residues providing coordinates for bonding (such as ionic, covalent, coordinative, hydrogen or Van der Waals bonding or combinations thereof) with organic or inorganic compounds. Useful additional amino acid sequences include, for example, poly-histidine residues useful for protein purification via Ni⁺-coupled residue, constant domains of immunoglobulins (IgA, IgE, IgG, IgM) or portions thereof (CH1, CH2, CH3), albumin, hemagluttinin (HA) or myc affinity epitope tags useful for the formation of immuno-complexes for detection or purification (antibodies against these moieties can be obtained commercially), polypeptides useful for detection such as the green fluorescent protein (GFP), enzymes such as beta-galactosidase (B-Gal), chloramphenicol acetyltransferase (CAT), luciferase, and alkaline phosphatase (A), signal sequences for protein trafficking and protease cleavage sequences useful for separating additional amino acid sequences from the sequence, if desired.

In an embodiment of the present invention, the isolated polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16.

A polypeptide according to embodiments of the present invention can be readily designed, synthesized and isolated using methods known in the art, in view of the present disclosure. The polypeptide can be produced as recombinant or naturally-occurring proteins by a method known to one skilled in the art. For example, a recombinant protein can be produced by a method comprising: (1) synthesizing a DNA encoding the protein using PCR with primers having desired restriction enzyme sites; (2) cloning the DNA into an expression vector, such as the pMAL-c2 expression vector (NEB); (3) transforming the expression vector into a host cell, such as Escherichia coli strain BL21 cell, to create a recombinant cell; (4) growing the recombinant cell under conditions to allow its expression of the recombinant protein; and (5) isolating the recombinant protein from the recombinant cell. The isolation of the recombinant protein can be facilitated by expressing the recombinant protein as a fusion protein with a histidine tag, maltose-binding protein, or glutathione-S-transferase (GST), and subsequently purifying or isolating the protein on a nickel column, an amylose-column, or a GST-glutathione column, respectively. After the purification or isolation, the above-described tag can be cleaved off using proteases, such as, thrombin and factor Xa as required.

When the polypeptide is produced and isolated as a naturally-occurring protein, such a protein is naturally produced by a plant or a plant tissue, and is isolated, for example, by binding an antibody to the polypeptide to an affinity column and contacting with the column an extract from the plant or plant tissue, such as rice or rice leaves, naturally expressing the polypeptide. The antibody can be prepared by immunizing a suitable animal with a partial sequence of the polypeptide made synthetically.

Another general aspect of the present invention relates to an isolated nucleic acid comprising a nucleotide sequence that encodes a mutant class C20 gibberellin 2-oxidase protein (GA2ox), or an isolated polypeptide comprising the mutant class C20 GA2ox.

The mutant C20 GA2ox has at least one mutation in domain III of a class C20 GA2ox and has a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation. The domain III, which comprises an amino acid sequence of SEQ ID NO:17, is one of the three unique and conserved amino acid domains that are present in the class C20 GA2oxs, but absent in the class C19 GA2oxs. It was discovered in the present invention that mutations in domain III affect the physiological activity of class C20 GA2oxs.

In an embodiment of the present invention, domain III comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23, and the otherwise identical class C20 GA2ox comprises an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26.

In view of the present disclosure, methods known in the art, such as site-directed mutagenesis (Kramer and Fritz, Methods in Enzymology, 154: 350-367 (1987)), can be used to introduce the at least one mutation, such as a deletion, insertion or substation of one or more amino acids, in domain III. The number and identity of amino acids that are mutated in domain III are not particularly restricted, as long as the class C20 GA2ox with the mutated domain III has a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation.

The enzymatic activity of a class C20 GA2ox with or without one or more mutations in domain III can be assayed using various methods known in the art in view of the present disclosure. For example, the class C20 GA2ox can be isolated or purified, e.g., from a recombinant cell that expresses the C20 GA2ox, or from a plant that has the C20 GA2ox. The enzymatic activity of the isolated or purified C20 GA2ox to hydroxylate a class C₂₀-GA precursor can be measured in vitro using a radio-labeled C₂₀-GA precursor, such as radio-labeled GA₁₂ or GA₅₃ (see Lee and Zeevaart, 2002; Schomburg et al., 2003). The enzymatic activity of the isolated or purified C20 GA2ox to hydroxylate a class C₂₀-GA precursor can also be measured in vivo by analyzing the amount of GA₁ or GA₉₇ in plant extracts, e.g., from the mature leaves or seedlings of plants containing the C20 GA2ox.

In an embodiment of the present invention, the mutant class C20 GA2ox comprises an amino acid sequence selected from the group consisting of:

-   -   (a) the amino acid sequence of SEQ ID NO:27, which has a         deletion of amino acid residues 335-341 of SEQ ID NO:2 (GA2ox5),         i.e., GA2ox5 Δ335-341;     -   (b) the amino acid sequence of SEQ ID NO:28, which has a         deletion of amino acid residues 325-341 of SEQ ID NO:2 (GA2ox5),         i.e., GA2ox5Δ325-341;     -   (c) the amino acid sequence of SEQ ID NO:29, which has a         deletion of amino acid residues 338-358 of SEQ ID NO:4 (GA2ox6),         i.e., GA2ox6Δ338-358;     -   (d) the amino acid sequence of SEQ ID NO:30, which has a         deletion of amino acid residues 348-358 of SEQ ID NO:4 (GA2ox6),         i.e., GA2ox6Δ348-358;     -   (e) the amino acid sequence of SEQ ID NO:68, which has a         deletion of amino acid residues 344-358 of SEQ ID NO:10         (GA2ox9-1), i.e., GA2ox9-1Δ344-359; and     -   (f) the amino acid sequence of SEQ ID NO:69, which has a         deletion of amino acid residues 354-358 of SEQ ID NO:10         (GA2ox9-1), i.e., GA2ox9-1Δ354-359.

Another general aspect of the present invention relates to an expression vector comprising a nucleotide sequence that encodes a polypeptide selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:2;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:4;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (e) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or SEQ ID NO:12;     -   (f) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or 16;     -   (g) a mutant class C20 GA2ox, the mutant GA2ox having at least         one mutation in domain III of class C20 GA2ox, the mutant GA2ox         having a reduced enzymatic activity to hydroxylate a class         C₂₀-GA precursor compared with an otherwise identical class C20         GA2ox that lacks the at least one mutation, and the domain III         comprising the amino acid sequence of SEQ ID NO:17.

The expression vectors comprise a nucleic acid according to embodiments of the invention in a form suitable for expression of the nucleic acid in a host cell. It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors according to embodiments of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein.

In an embodiment of the present invention, the expression vector is replicable and confers a selective marker in a plant cell. In another embodiment of the present invention, the expression vector is replicable and confers a selective marker in an Agrobacterium, a bacterium known for its ability to transfer nucleic acid between itself and plants. In yet another embodiment of the present invention, the expression vector allows the shuttling or exchange of nucleotide sequences between a plant cell and an Agrobacterium. Such expression vectors can be a modified bacterial tumor-inducing (Ti) plasmid or a bacterial root-inducing (Ri) plasmid.

In an embodiment of the present invention, the expression vector comprises a nucleotide sequence that encodes a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16.

In another embodiment of the present invention, the expression vector comprises a nucleotide sequence that encodes a mutant class C20 GA2ox comprising an amino acid sequence selected from the group consisting of: SEQ ID NOs:27-30, SEQ ID NO:68 and SEQ ID NO:69.

Any of a variety of procedures known in the art, such as electroporation, calcium phosphate precipitation, polyethylene glycol transformation, microinjection, nanoparticle-mediated transformation, particle bombardment, Agrobacterium-mediated transfer, biolistics-mediated transfomation and viral infection, can be used to introduce an expression vector into a host cell in view of the present disclosure.

In another general aspect, the present invention relates to a recombinant cell comprising a nucleotide sequence according to embodiments of the invention. In one embodiment, the recombinant cell is a recombinant plant cell, which includes various forms of plant cells, such as cultured cell suspensions, protoplasts, leaf sections and calluses. In another embodiment, the recombinant cell is a recombinant Agrobacterium cell. In another embodiment, the recombinant cell comprises an expression vector according to embodiments of the present invention. In an embodiment of the present invention, the recombinant cell comprises a nucleotide sequence that encodes a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NOs:27-30, SEQ ID NO:68 and SEQ ID NO:69.

Any of a variety of procedures known in the art can be used to construct a recombinant cell according to embodiments of the present invention. For example, a nucleotide sequence according to embodiments of the invention can be introduced into a host cell via a vector. The nucleotide sequence can stay on the vector, separate from the chromosome, in the recombinant cell, such as in a transiently transfected recombinant cell that transiently expresses a gene product encoded by the nucleotide sequence. The nucleotide sequence can also be integrated into the chromosome in the recombinant cell, such as in a stably transfected recombinant cell that stably expresses a gene product encoded by the nucleotide sequence.

In another general aspect, the present invention relates to a transgenic plant comprising a transgene, wherein the transgene encodes a polypeptide selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:2;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:4;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (e) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or at least about 80%         identical to SEQ ID NO:12;     -   (f) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or at least about 80%         identical to SEQ ID NO:16;     -   (g) a mutant class C20 GA2ox, the mutant GA2ox having at least         one mutation in domain III of class C20 GA2ox, the mutant GA2ox         having a reduced enzymatic activity to hydroxylate a class         C₂₀-GA precursor compared with an otherwise identical class C20         GA2ox that lacks the at least one mutation, and the domain III         comprising the amino acid sequence of SEQ ID NO:17.

In an embodiment of the present invention, the transgenic plant comprises the mutant class C20 GA2ox, wherein

-   -   (a) the domain III comprises an amino acid sequence selected         from the group consisting of SEQ ID NOs:18-23; and     -   (b) the otherwise identical class C20 GA2ox comprises an amino         acid sequence selected from the group consisting of: SEQ ID         NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:24, SEQ ID NO:25, and         SEQ ID NO:26.

In a preferred embodiment of the present invention, the transgenic plant comprises a transgene, which encodes a polypeptide having the amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NOs:27-30, SEQ ID NO:68 and SEQ ID NO:69.

In one embodiment, a transgenic plant according to embodiments of the present invention stably expresses a gene encoded by a recombinant nucleic acid molecule according to embodiments of the invention. In such a transgenic plant, the recombinant nucleic acid molecule is stably transformed or transfected into a plant cell and has become integrated into the chromosome of the plant cell so that the recombinant nucleic acid molecule is inherited by daughter cells of the plant cell through chromosome replication.

Any of a variety of procedures known in the art can be used to engineer a stable transgenic plant in view of the present disclosure. In one embodiment of the present invention, the transgenic plant is constructed by transforming a tissue of a plant, such as a protoplast or leaf-disc of the plant, with a recombinant Agrobacterium cell comprising a nucleic acid molecule according to embodiments of the present invention, and generating a whole plant using the transformed plant tissue. In another embodiment of the present invention, flowers of a plant can be dipped in a culture of recombinant Agrobacterium cell comprising a nucleic acid molecule according to embodiments of the present invention. After the bacterium transforms the germline cells that make the female gametes, seeds can be screened for markers carried by the nucleic acid molecule according to embodiments of the present invention. Transgenic plants are then grown out of the seeds.

In another embodiment of the present invention, a nucleic acid molecule according to embodiments of the invention can be introduced into a plant via gene gun technology, particularly when transformation with a recombinant Agrobacterium cell is less efficient in the plant. The gene gun technology, also referred to as biolistics, delivers genetic information via an elemental particle of a heavy metal coated with plasmid DNA. This technology is able to transform almost any type of plant cells.

In another embodiment, a transgenic plant according to embodiments of the present invention transiently expresses a gene encoded by a recombinant nucleic acid molecule according to embodiments of the invention. Any of a variety of procedures known in the art can be used to engineer such a transgenic plant in view of the present disclosure. In one embodiment, a recombinant nucleic acid molecule according to embodiments of the invention can be introduced into a transgenic plant by particle bombardment, a specific example of which is described below in the examples. In another embodiment, the method of agroinfiltration can be used to allow transient expression of genes in a plant. In the method, for example, a recombinant nucleic acid molecule according to embodiments of the invention is first introduced into a strain of Agrobacterium to generate a recombinant Agrobacterium cell. A liquid suspension of the recombinant Agrobacterium is then injected into the airspaces inside a plant leaf. Once inside the leaf, the recombinant Agrobacterium transforms the gene of interest to a portion of the plant cells and the gene is then transiently expressed. As compared to traditional plant transformation, the method of agroinfiltration is speedy and convenient.

The transgenic plant according to embodiments of the present invention can be both monocot and dicot transgenic plants. In an embodiment of the present invention, the transgenic plant is a transgenic cereal plant, preferably a transgenic rice plant.

The transgenic plant according to embodiments of the present invention can comprise a transgene that is operably linked to any suitable promoters known in the art to provide a control point for regulated gene transcription of the transgene in the transgenic plant. The promoters that can be used in the present invention, include, but are not limited to a native promoter; a constitutive promoter selected from the group consisting of a maize ubiquitin (Ubi) promoter, a rice actin (Act1) promoter, and cauliflower mosaic 35S RNA promoter (CaMV35S) promoter; a tissue-specific promoter selected from the group consisting of a rice glutelin (GluB) promoter, a rubisco small subunit (rbcS) promoter and a maize zean gene promoter; a developmental stage-specific promoter selected from the group consisting of a rice alpha-amylase (αAmy) promoter and a rice glycine rich RNA binding protein (GRRP-A1) promoter; and an inducible promoter inducible by drought, salt, high or low temperatures, hypoxia, anoxia, hydration, pH, chemicals, or hormones. Examples of the inducible promoters that can be used in the present invention, include, but are not limited to, promoters for the genes of Arabidopsis rd29A, cor15A, kin1, heat-shock factor (HSF), C-repeat-binding factor (CBF1) and dehydration-responsive element binding protein (DREB1A); and promoters for the genes of rice HVA1 (ABA-inducible), alcohol dehydrogenase (Adh), ethanol-inducible, and alpha-amylase (GA-inducible).

In an embodiment of the present invention, the promoter is expressed in developing seeds, during seed germination, in early seedlings, or in growing plants.

In another embodiment of the present invention, the transgenic plant is at least about 10% shorter, or has more root system, earlier tillering, higher tillering numbers, higher biomass, or higher seed production, than a non-transgenic plant of the same genetic background while being grown under the same conditions. Tillering is an important agronomic trait for grain yield. The tiller is a specialized grain-bearing branch that normally arises from the axil of each leaf and grows independently of the mother stem (culm) with its own adventitious roots. The present invention demonstrates that plant architecture improvements, including, but not limited to semidwarfism, increased root system and higher tiller numbers, which favor grain yield, could be induced by increased expression or activity of wild-type or modified C19 GA2oxs or C20 GA2oxs.

In a preferred embodiment, the transgenic plant is a semi-dwarf or dwarf transgenic plant having a height that is about 20% to 90% of a non-transgenic plant of the same genetic background while being grown under the same conditions. In particular embodiments, the transgenic plant is a semi-dwarf or dwarf transgenic plant having a height that is about 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% of that of a non-transgenic plant of the same genetic background while being grown under the same conditions.

An embodiment of the present invention also includes a propagation material obtained from the transgenic plant according to embodiments of the present invention, wherein the propagation material contains the transgene.

In another general aspect, the present invention relates to a method of producing a transgenic plant of the present invention. The method comprises: (a) transforming a plant cell with a nucleic acid molecule comprising the transgene according to an embodiment of the present invention to obtain a recombinant plant cell; and (b) growing the recombinant plant cell obtained in (a) to generate a transgenic plant.

Another general aspect of the present invention relates to a method of inhibiting stem elongation and promoting tiller growth in a plant. The method comprises: (a) transforming a plant cell with a nucleic acid molecule comprising a transgene according to an embodiment of the present invention to obtain a recombinant plant cell that expresses a polypeptide encoded by the transgene; and (b) growing the recombinant plant cell obtained in (a) to generate a transgenic plant; wherein the polypeptide is expressed in the transgenic plant at a level sufficient to inhibit stem elongation and promote tiller growth in the transgenic plant.

In another embodiment of the method of the present invention, the transgene encodes a mutant class C20 GA2ox having at least one mutation in domain III of the class C20 GA2ox. The mutant GA2ox has a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation. Preferably, the domain III comprises an amino acid sequence selected from the group consisting of SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22 and SEQ ID NO:23, and the otherwise identical class C20 GA2ox that lacks the at least one mutation comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26.

According to an embodiment of the present invention, the transgene used in the method encodes a polypeptide selected from the group consisting of a polypeptide having the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:27, SEQ ID NO:30 and SEQ ID NO:69.

According to an embodiment of the present invention, the transgene can be overexpressed in the transgenic plant, i.e., is expressed at a level higher than that of an otherwise identical gene in a non-transgenic plant of the same genetic background. For example, the transgene encoding SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:28, or SEQ ID NO:29 was overexpressed in transgenic rice plants according to embodiments of the invention.

According to another embodiment of the present invention, the transgene can be expressed at a level the same as or lower than that of an otherwise identical gene in a non-transgenic plant of the same genetic background. For example, the transgene encoding SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:27, SEQ ID NO:30 or SEQ ID NO:69 was not overexpressed in transgenic rice plants according to embodiments of the invention.

According to a preferred embodiment of the present invention, the method further comprises breeding the transgenic plant with another plant to obtain a semi-dwarf or dwarf transgenic plant that still contains the transgene. Preferably, the transgenic plant is a severely dwarf transgenic plant and the other plant is a non-transgenic plant of the same genetic background. The breeding of the severely dwarf transgenic plant with the non-transgenic plant can produce a semi-dwarf or dwarf transgenic plant that is less dwarf than the severely dwarf parent transgenic plant. More preferably, the transgene in the transgenic plant encodes a polypeptide selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8 and SEQ ID NO:10.

According to another preferred embodiment of the present invention, the transgene used in the method encodes a polypeptide selected from the group consisting of a polypeptide having the amino acid sequence of SEQ ID NO:10, SEQ ID NO:27, SEQ ID NO:30 and SEQ ID NO:69, and the polypeptide is expressed in the transgenic plant at a level sufficient to inhibit growth and make a semi-dwarf transgenic plant.

Another general aspect of the present invention relates to a method of obtaining a semi-dwarf transgenic plant. The method comprises: (a) providing a transgenic plant according to embodiments of the present invention or a propagation material thereof; (b) growing the transgenic plant or the propagation material thereof, so that the polypeptide transgenically or recombinantly expressed in the transgenic plant is at a level sufficient to inhibit growth of the transgenic plant; and (c) applying to the transgenic plant or the propagation material thereof a composition comprising at least one bioactive GA compound, so that the transgenic plant or propagation material thereof produces a semi-dwarf transgenic plant. The bioactive GA compound can be applied directly to the transgenic plant or the propagation material or indirectly to the soil in which the transgenic plant or the propagation material is grown.

The transgene expressed in the transgenic plant can be any of the transgene according to embodiments of the present invention. In an embodiment of the present invention, the transgene encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8 or SEQ ID NO:10. In a preferred embodiment, the transgene is overexpressed in the transgenic plant.

The bioactive GA compound can be any bioactive GA compounds. In an embodiment of the present invention, the bioactive GA compound is not inactivated by the polypeptide recombinantly produced by the transgenic plant. Preferably, the bioactive GA compound is selected from the group consisting of GA₁, GA₃, GA₄ and GA₇.

Another general aspect of the present invention relates to a method of inhibiting stem elongation and promoting tiller growth in a plant, comprising administering to the plant a compound that increases the expression of a gene encoding a polypeptide or the enzymatic activity of the polypeptide in the plant, wherein the polypeptide is selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:2;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:4;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (e) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or at least about 80%         identical to SEQ ID NO:12; and     -   (f) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or at least about 80%         identical to SEQ ID NO:16.

In a preferred embodiment, the polypeptide is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, and the plant is a rice plant.

The compound that increases the expression of a gene encoding a polypeptide or the enzymatic activity of the polypeptide in the plant can be of any type, including, but not limited to a small molecule chemical compound and a molecule of biological origin, i.e., that is originally identified as a molecule made by a biological system, such as a plant, a microorganism, etc., or derivatives thereof.

Another general aspect of the present invention relates to a method of identifying a compound that inhibits stem elongation and promotes tiller growth in a plant, comprising identifying a compound that increases the expression of a gene encoding a polypeptide or the enzymatic activity of the polypeptide in the plant, wherein the polypeptide is selected from the group consisting of:

-   -   (a) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:2;     -   (b) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:4;     -   (c) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:6;     -   (d) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:8;     -   (e) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:10 or at least about 80%         identical to SEQ ID NO:12; and     -   (f) a polypeptide having an amino acid sequence that is at least         about 80% identical to SEQ ID NO:14 or at least about 80%         identical to SEQ ID NO:16.

In a preferred embodiment, the polypeptide is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8 and SEQ ID NO:10, and the plant is a rice plant.

Various methods can be used to facilitate the identification of the compounds. For example, in vitro assay, preferably high-though put assay, can be conducted using an isolated polypeptide to identify compounds that increase the enzymatic activity of the polypeptide. Such in vitro assay can be based on the enzymatic activity of a C19 GA2ox, such as GA2ox7, GA2ox8 or GA2ox10, to hydroxylate the C-2 of biologically active C₁₉-GAs (GA₁ and GA₄) or C₁₉-GA precursors (GA₂₀ and GA₉) to produce biologically inactive GAs (GA₈, GA₃₄, GA₂₉, and GA₅₁, respectively). The in vitro assay can also be based on the enzymatic activity of a C20 GA2ox, such as GA2ox5, GA2ox6 or GA2ox9, to catalyze 2β-hydroxylation of C₂₀-GA precursors, e.g., converting GA₁₂ and GA₅₃ to GA₁₁₀ and GA₉₇, respectively. The enzymatic activity of a C19 GA2ox or C20 GA2ox can be measured using methods known to those skilled in the art, for example, by using a radio-labeled C₁₉-GA, C₁₉-GA precursor or C₂₀-GA precursor.

Compounds that increase the expression of a gene of interest can be identified using a cell based reporter assay. The transcriptional regulatory region of a gene according to an embodiment of the present invention, including the promoter and the 5′- and/or 3′-untranslated regulatory (UTR) region of the gene, can be operably linked to the coding sequence of a reporter gene, such as a luciferase gene (lux), a β-galactosidase gene (lacZ), a green fluorescent protein gene (GFP), etc. The expression level of the gene can thus be more easily measured from a cell as the biological activity of the reporter gene product. A compound that increases the expression of the gene can be identified by its ability to increase the detected amount of the biological activity of the reporter gene product from the reporter assay.

The compound can be further identified using an in vivo assay, e.g., by administering the compound to a plant and analyzing the amount of biologically inactive GAs in plant extracts.

This invention will be better understood by reference to the non-limiting examples that follow, but those skilled in the art will readily appreciate that the examples are only illustrative of the invention as described more fully in the claims which follow thereafter.

Identification of the Rice GA2ox Family

The preliminary computer search of the rice genome has identified 10 putative GA2ox genes. Three members of this gene family in rice had previously been found to encode GA2oxs with three unique and conserved domains, as with the class C20 GA2oxs of Arabidopsis and spinach (Lee and Zeevaart, 2005). Questions were thus raised as to whether all predicted rice GA2oxs are differentially expressed and regulated, and what their physiological functions in rice are.

Putative rice GA2oxs were sought by BLAST searching the NCBI, TIGR, and RiceGAAS databases with the conserved domain in the 2-oxoglutarate (2OG) and Fe (III)-dependent oxygenase family and nucleotide sequences of four previously identified rice GA2oxs (GA2ox1 to GA2ox4). A total of 10 putative GA2oxs were identified (Table 1). Among them, GA2ox1 to GA2ox4 had previously been partially characterized (Sakamoto, et al., 2001, 2004; Sakai et al., 2003), and GA2ox5 and GA2ox6 had been reported but remained uncharacterized (Lee and Zeevaart, 2005). Four other GA2oxs, designated here as GA2ox7 to GA2ox10, were identified in this study. Almost all GA2oxs encoded 300 to 400 amino acid residues, including the 2OG-Fe (II) oxygenase conserved domain. However, the predicted PI value of GA2ox10 is 9.3, which is significantly different from those of other GA2oxs with predicted PI values ranging from 5.0˜7.2.

TABLE 1 Putative GA2ox gene family in rice (Oryza sativa) Gene Accession PI Amino Name Chromosome BAC No. Site^(a) Locus^(b) no. of cDNA value acid GA2ox1 5 OSJNBa0017J22  8748~34623 LOC_Os05g06670 AK120967 6.52 403 GA2ox2 1 B1140D12  9818~19799 LOC_Os01g22910 6.64 370 GA2ox3 1 OJ1414_E05 66551~68322 LOC_Os01g55240 AK101713 6.26 327 GA2ox4 5 P0022D06 49345~50496 LOC_Os05g43880 AK107211 6.39 354 GA2ox5 7 P0446F04 52078~53103 LOC_Os07g01340 AK106859 5.88 341 GA2ox6 4 OSJNBa0019D11 138689~141990 LOC_Os04g44150 7.18 358 GA2ox7 1 P0466B10 35930~39272 LOC_Os01g11150 AK108802 6.67 335 GA2ox8 5 OJ1115_B06 55485~57032 LOC_Os05g48700 AK101758 6.03 353 GA2ox9 2 B1469H02 122528~120151 LOC_Os02g41954.1 Ak059045 5.58 359 LOC_Os02g41954.2 AK108598 5.04 299 GA2ox10 5 OSJNBb0016G07  9180~13210 LOC_Os05g11810.1 9.37 378 LOC_Os05g11810.2 9.33 271 ^(a)The critical site of BAC clone. ^(b)Locus was identified by the TIGR Rice Pseudomolecules and Genome Annotation 5.0 (www.tigr.org/tdb/e2kl/osal/), but the relative cDNA clone of GA2ox10 could not be found. GA2ox1 to GA2ox4 were identified by Sakamoto et al. (2001, 2004). GA2ox5 and GA2ox6 were nominated by Lee and Zeevaart (2005). GA2ox7 to GA2ox11 were nominated in this study, based on the sequence similarity search and gene annotation using the NCBI, TIGR and RiceGAAS databases.

The locations of GA2oxs in the rice genome were determined, with seven GA2oxs clustered on chromosome 1 and 5 and others located on chromosomes 2, 4, and 7 (FIG. 1A). Amino acid sequence comparison (Table 2) generated a phylogenetic tree among the rice GA2ox family (FIG. 1B). GA2oxs located on the same chromosome have more amino acid sequence divergence from each other than from GA2oxs located on different chromosomes, indicating that gene duplication by crossing-over among chromosomes has occurred throughout their evolution.

TABLE 2 Comparison of deduced amino acids among rice GA2oxs GA2ox5 GA2ox6 GA2ox9 GA2ox1 GA2ox2 GA2ox10 GA2ox7 GA2ox3 GA2ox4 GA2ox8 GA2ox5 100 62 63 38 43 22 47 50 47 45 GA2ox6 100 76 36 41 20 44 46 44 44 GA2ox9 100 34 39 19 43 45 42 42 GA2ox1 100 66 24 49 50 49 51 GA2ox2 100 32 56 57 56 57 GA2ox10 100 41 38 35 35 GA2ox7 100 70 63 64 GA2ox3 100 73 70 GA2ox4 100 67 GA2ox8 100

Amino acid sequence comparison also generated a phylogenetic tree of 10 rice GA2oxs and 19 GA2oxs from 8 dicot plant species (Table 3), which revealed that rice GA2ox5, GA2ox6 and GA2ox9 are more closely related to the Arabidopsis GA2ox7 and GA2ox8 and spinach GA2ox3 (FIG. 1C). These six GA2oxs contain three unique and conserved domains (Lee and Zeevaart, 2005) (FIG. 11).

TABLE 3 Gene names and accession number of 19 GA2oxs from different plant species Name Species Accession Number AtGA2ox1 Arabidopsis thaliana AJ132435 AtGA2ox2 Arabidopsis thaliana AJ132436 AtGA2ox3 Arabidopsis thaliana AJ132437 AtGA2ox4 Arabidopsis thaliana AY859740 AtGA2ox6 Arabidopsis thaliana AY859741 AtGA2ox7 Arabidopsis thaliana NM103976 AtGA2ox8 Arabidopsis thaliana NM118239 CmGA2ox Cucurbita maxima AJ302041 LsGA2ox1 Lactuca sativa AB031206 NtGA2ox1 Nicotiana sylvestris AB125232 NtGA2ox3 Nicotiana sylvestris EF471117 NtGA2ox5 Nicotiana sylvestris EF471118 PcGA2ox1 Phaseolus coccineus AJ132438 Poplar GA2ox1 Populus alba x P. tremuloides AY392094 PsGA2ox1 Pisum sativum AF056935 PsGA2ox2 Pisum sativum AF100954 SoGA2ox1 Spinacia oleracea AF506281 SoGA2ox2 Spinacia oleracea AF506282 SoGA2ox3 Spinacia oleracea AY935713

Differential Expression of GA2ox Correlated With Flower and Tiller Development

Growth of the rice cultivar TNG67 used in the present study could be divided into vegetative, reproductive and ripening phases (FIG. 2A). To understand the role that individual GA2oxs may play in rice growth, the temporal expression patterns of GA2oxs in rice during the rice life cycle was examined. As leaves have been shown to be a major site of GA biosynthesis (Choi et al., 1995), fully expanded leaves at different growth or developmental stages ranging from 5 to 100 days after imbibition (DAI) were collected. The different growth or developmental stages include seedling from about 1-20 DAI, tillering from about 30-40 DAI, reproductive from about 60-90 DAI and ripening at about 100 DAI. Total RNAs were isolated from the leaves. The expression levels of GA2ox mRNA were analyzed by RT-PCR using GA2ox and GA3ox2 gene-specific primers (Table 7), and the 18S rRNA gene (rRNA) was used as a control.

It was observed that the genes GA2ox1 to GA2ox9 were differentially expressed in leaves and the expression was temporally regulated. However, mRNAs of GA2ox10 was not detected in any tissue in any growth stage, indicating GA2ox10 may be a pseudogene or its mRNA level was too low to be detected. Based on temporal mRNA accumulation patterns, the GA2oxs could be classified into 2 groups. As can be seen in FIG. 2B, for members of group A, which exclude GA2ox2 and GA2ox6, accumulation of their mRNAs in leaves was detected prior to the transition from vegetative to reproductive growth phases. In contrast, for members of group B, which include GA2ox2 and GA2ox6, their mRNAs accumulated in leaves after the phase transition from vegetative to reproductive growth. GA2ox6 mRNA could also be detected in leaves at early seedling stage and transiently at high level during active tillering stage.

Since expression of most GA2oxs terminated after tillering, the pattern of tiller growth throughout the rice life cycle was examined. Tiller number increased from 30 to 50 DAI, remained constant until 75 DAI, and then increased again until 90 DAI when the experiment was terminated (FIG. 2C). Expression of group A and group B GA2oxs paralleled the increase in tiller number in the vegetative and reproductive phases, respectively (FIG. 2, compare B with C). Except for a slight reduction in the reproductive phase, the expression of GA3ox2, which encodes the enzyme involved in GA biosynthesis, was not significantly altered in leaves throughout the rice life cycle. These results suggest that up- and down-regulation of group A GA2oxs may control GA levels for tiller growth in the vegetative phase and for flower development in the reproductive phase, respectively, while up-regulation of group B GA2oxs controls tiller growth in the reproductive phase.

Decrease in GA2ox6 Expression Correlated With Seed Germination

Bioactive-GAs are well-known to be responsible for relieving seed dormancy and promoting germination, so the role of GA2oxs during germination was studied. Seeds were imbibed for various lengths of time. Germination of wild-type seeds was observed from 1 DAI which reached almost 100% at 2 DAI (FIG. 3A). Total RNAs were isolated from embryos after imibibition of seeds, and temporal expression profiles of six GA2oxs were analyzed by RT-PCR. Accumulation of most GA2ox mRNAs was detectable starting from 0 to 1 DAI, which was maintained at similar levels afterward (FIG. 3B). GA2ox6 had a distinct expression pattern as its mRNA quickly accumulated from 0.5 to 1 DAI and then decreased significantly from 2 to 4 DAI. Low-level accumulation of GA3ox mRNA was detected at 0 DAI and then at similarly high levels after 0.5 DAI. This study demonstrated that most GA2oxs were constitutively expressed and competed with GA3ox for GA, while only GA2ox6 was transiently expressed and its reduced expression correlated with the rapid seed germination at 2 DAI.

Plant Growth and Seed Germination Were Impaired in T-DNA Tagged Rice Mutants Overexpressing GA2oxs

To study the functions of GA2oxs in rice, mutants in a T-DNA tagged rice mutant library, the Taiwan Rice Insertional Mutagenesis (TRIM) library (Hsing et al., 2007), were screened. The T-DNA tag used for generating the TRIM library contained multiple CaMV35S enhancers adjacent to the right border, which activate promoters located close to T-DNA insertion sites (Hsing et al., 2007). Two GA2ox-activated dwarf mutants, M77777 and M47191, were identified by a forward genetic screen and another two mutants, M27337 and M58817, were identified by a reverse genetic screen of the library (FIG. 4).

The severely dwarf mutant M77777, designated as GA2ox3_(ACT), carries a T-DNA insertion at a position 587 bp upstream of the translation start codon of GA2ox3 (FIG. 4A). Accumulation of GA2ox3 mRNA in this mutant was significantly enhanced in the heterozygous mutant. GA2ox3_(ACT) mutant did not produce seeds and was therefore maintained and propagated vegetatively.

The semi-dwarf mutant M27337, designated as GA2ox5 Δ335-341_(ACT), carries a T-DNA insertion in the coding region, at a position 23 bp upstream of the translation stop codon of GA2ox5 (FIG. 4B). Truncation of GA2ox5 by T-DNA resulted in a loss of 4 amino acids at the C-terminal of the putative GA2ox5 polypeptide. Accumulation of the truncated GA2ox5 mRNA was significantly enhanced by T-DNA activation tagging in both homozygous and heterozygous mutants, but the semi-dwarf phenotype was observed only in the homozygous mutant. The GA2ox5 Δ335-341_(ACT) homozygous mutant had an average plant height 90%, and produced seeds with an average fertility 88%, of the wild type (Table 4). These results suggest that the truncated GA2ox5 mRNA might encode a partially functional GA2ox5.

TABLE 4 Characterization of rice mutants and transgenic rice overexpressing GA2oxs GA2ox5Δ335-341_(ACT) GA2ox9_(ACT) GA2ox6_(ACT) Ubi::GA2ox5 Ubi::GA2ox6 Traits Wild type (T3)^(a) (T3) (T2) (T1) (T1) Tiller number of  1.0 ± 0.0^(b)  1.8 ± 0.8  1.0 ± 0.0 2.6 ± 0.5 2.7 ± 0.6 2.5 ± 0.7 seedling (18 DAI)   (100)^(c) (180) (100)  (260)  (270)  (250)  Root length (cm) at  6.3 ± 0.9 15.7 ± 3.2 11.0 ± 1.9 5.8 ± 1.8 6.3 ± 2.1 6.6 ± 0.4 18 DAI (100) (249) (175)  (92) (100)  (105)  Plant height (cm) 109.5 ± 2.5  98.0 ± 7.1 83.2 ± 4.1 16.6 ± 1.7  16.7 ± 2.8  12.1 ± 2.7  at 120 DAI (100)  (90) (76) (15) (15) (11) Length of the leaf 49.9 ± 6.0 49.6 ± 5.1 49.3 ± 3.3 12.2 ± 0.9  10.6 ± 1.2  8.1 ± 0.8 below flag leaf (100) (100) (99) (24) (21) (16) (cm) at 120 DAI Width of the leaf 1.64 ± 0.1 1.66 ± 0.1 1.75 ± 0.2 1.51 ± 0.1  1.2 ± 0.1 1.04 ± 0.1  below flag leaf (100) (101) (107)  (92) (73) (63) (cm) at 120 DAI Heading day (DAI) 108.7 ± 1.5  107.6 ± 1.3  107.9 ± 1.0  >150  >150  >150  Panicle length (cm) 21.6 ± 2.0 20.3 ± 1.5 19.7 ± 1.8 7.7 ± 1.6 5.9 ± 0.8 7.5 ± 0.9 (100)  (94) (91) (36) (27) (35) Final Tiller number 11.0 ± 1.8 20.3 ± 4.1 13.4 ± 2.9 17.6 ± 3.7  NA 18.8 ± 4.5  (100) (185) (122)  (160)  (171)  Grain weight 2.44 ± 0.1 2.04 ± 0.1 2.34 ± 0.2 1.54 (63) 1.43 (59) 1.98 (81) (g/100 grains) (100)  (84) (96) Fertility (%) 92.6 ± 4.2 81.1 ± 5.4 85.4 ± 8.9 39.5 ± 18  27.7 ± 12.0 59.4 ± 4.4  (100)  (88) (92) (43) (30) (64) ^(a)T1, T2 and T3 in parenthesis indicate generation of mutants. ^(b)SE; n = 20 for GA2ox5Δ335-341_(ACT), GA2ox9_(ACT), and GA2ox6_(ACT); n = 10 for Ubi::GA2ox5 and Ubi::GA2ox6. ^(c)Values in parentheses indicate % of the wild type. NA: not available. DAI: days after imbibition.

The severely dwarf mutant M47191, designated as GA2ox6_(ACT), carries a T-DNA insertion at a position 2.1 kb upstream of the translation start codon of GA2ox6 (FIG. 4C). Accumulation of GA2ox6 mRNA was significantly enhanced by T-DNA activation tagging, and severely dwarf phenotype was observed in both heterozygous and homozygous mutants. The GA2ox6_(ACT) homozygous mutant produced seeds with an average fertility of only 43% of the wild type after more than 5 months of growth (Table 4).

The semi-dwarf mutant M58817, designated as GA2ox9_(ACT), carries a T-DNA insertion at a position 2.4 kb upstream of the translation start codon of GA2ox9 (FIG. 4D). Accumulation of GA2ox9 mRNA was significantly enhanced by T-DNA activation tagging, and the semi-dwarf phenotype was observed in both homozygous and heterozygous mutant. The GA2ox9_(ACT) homozygous mutant produced seeds with an average fertility of 92% of the wild type (Table 4).

The three activation-tagged mutants, GA²ox5 Δ335-341_(ACT), GA2ox6_(ACT) and GA2ox9_(ACT), were further characterized. Mutant seedlings and plants displayed the same phenotypes as their parents, with GA2ox5 Δ335-341_(ACT) growing slightly shorter and GA2ox9_(ACT) shorter still than the wild type, while GA2ox6_(ACT) remained severely dwarfed throughout all growth stages (FIGS. 5, A and B). GA2ox5 Δ335-341_(ACT) and GA2ox9_(ACT) displayed a rather normal phenotype, except for longer roots and higher tiller numbers than the wild type (Table 4). Other phenotypes significantly altered in the severely dwarf GA2ox6_(ACT) mutant included shorter leaf length, longer heading day, shorter panicle length, higher tiller numbers, lower grain weight and lower seed fertility as compared with the wild type (Table 4). Germination of GA2ox6_(ACT) seeds was also significantly delayed, as it took 20 days to reach 90% germination rate, while the wild type and GA2ox9_(ACT) mutant seeds took only 2 days to reach a germination rate of 97% and 98%, respectively (FIG. 5C). Germination of GA2ox5 Δ335-341_(ACT) seeds was delayed for 4 days to reach a final 88% germination rate (FIG. 5C).

Overexpression of GA2ox5 and GA2ox6 Recapitulated the Dwarf or Semi-Dwarf Phenotypes in Transgenic Rice and Tobacco

To verify the function of GA2ox5 and GA2ox6 in dwarfism of rice plants, full length cDNAs of GA2ox5 and GA2ox6 were isolated from rice and fused downstream of the maize ubiquitin (Ubi) promoter, generating Ubi::GA2ox5 and Ubi::GA2ox6 constructs for rice transformation. More than 30 independent transgenic rice lines were obtained for each construct. All transgenic rice plants showed dwarf phenotypes, although slight variations in final height were observed. The overall phenotypes of Ubi::GA2ox5 and Ubi::GA2ox6 T₁ plants were similar to the GA2ox6_(ACT) mutant, except that the seed fertility produced by Ubi::GA2ox6 transgenic rice (average 64%) was higher than of Ubi::GA2ox5 transgenic rice (average 30%) (FIGS. 6, A and B and Table 4). RT-PCR analysis showed that both GA2ox5 and GA2ox6 mRNAs accumulated at similar high levels in all transgenic lines (data not shown). These results demonstrated that ectopic overexpression of GA2ox5 or GA2ox6 was able to recapitulate the dwarf phenotype in transgenic rice. They also suggest that the nearly normal phenotype of GA2ox5 Δ335-341_(ACT) mutant could be due to overexpression of a GA2ox5 product missing part of domain III.

Ectopic overexpression of Arabidopsis GA2ox7 and GA2ox8 and spinach GA2ox3 reduced the bioactive GA content and resulted in a dwarf phenotype of transgenic tobacco plants (Schomburg et al., 2003: Lee and Zeevaart, 2005). To examine whether rice GA2oxs are also functional in dicots, Ubi::GA2ox5 and Ubi::GA2ox6 constructs were used for tobacco transformation.

Ectopic overexpression of these two rice GA2oxs in transgenic tobacco revealed the same retardation of plant growth, but with different effects. While Ubi::GA2ox5 reduced plant height to 32% and seed production to 62%, and Ubi::GA2ox6 reduced plant height to 67% of the wild type tobacco, Ubi::GA2ox6 had no effect on seed production (FIGS. 6C and D, upper panels, and Table 5). The numbers of leaves to inflorescence were not different between the transgenic and wild type tobacco, but the flowering time was delayed approximately 2 to 4 weeks for all transgenic tobacco. Growth of hypocotyls and roots of 18-day-old T₁ transgenic tobacco seedlings was slightly retarded by overexpression of GA2ox6, but significantly retarded by overexpression of GA2ox5, compared with the wild type (FIGS. 6C and D, lower panels, and Table 5). These studies demonstrated that the two rice GA2oxs have similar functions in monocots and dicots, with GA2ox5 being more potent in inactivation of GA than GA2ox6 in both transgenic rice and tobacco.

TABLE 5 Characterization of transgenic tobacco overexpressing rice GA2ox5 and GA2ox6 Traits Wild Type Ubi::GA2ox5 Ubi::GA2ox6 Root length (mm) at 18  20.8 ± 2.7^(a) (100)^(b)  9.6 ± 4.6 (46) 17.7 ± 3.6 (85) DAI Hypocotyl length (mm) at  6.5 ± 0.8 (100)  3.2 ± 0.6 (49)  4.6 ± 1.0 (71) 18 DAI Final Plant height (cm) 127.7 ± 4.7 (100) 41.2 ± 18.9 (32) 85.3 ± 9.4 (67) Number of leaves to  18.3 ± 0.6 (100) 20.8 ± 3.3 (114) 19.0 ± 0.8 (104) inflorescence Seeds yield (g)/plant 31.1 (100) 19.3 ± 3.4 (62) 31.3 ± 4.1 (100) ^(a)SE with n = 40. ^(b)Values in parentheses indicate % of the wild type.

Overexpression of GA2ox6 Reduced GA Levels in Rice Mutants in Which Only Shoot But Not Root Growth was Affected

To determine whether the dwarfism of rice mutants overexpressing GA2ox was a result of a reduction of bio-active GAs, GA2ox6_(ACT) mutant seeds were germinated on MS agar medium with or without supplementation with 5 μM GA₃. Addition of GA₃ promoted germination of GA2ox6_(ACT) seeds (FIG. 7A), indicating that an insufficient endogenous GA concentration was responsible for the reduced germination of GA2ox6_(ACT) mutant seeds. Plant height of 18-day-old wild-type seedlings was only slightly enhanced by GA₃ treatment; in contrast, height of the dwarf GA2ox6_(ACT) mutant seedlings was significantly enhanced by GA₃ treatment, with recovery of up to 84% of the wild type (FIG. 7B). Root lengths of the wild type and GA2ox6_(ACT) mutant seedlings were similar, and both were effectively enhanced by GA₃ treatment (FIG. 7B).

It was noticed that root growth of GA2ox6_(ACT) was significantly slower initially after germination (FIG. 7A, upper panel), but it sped up after 6 DAI and became similar to the wild type at 18 DAI (FIG. 7B). A similar phenomenon was observed for other mutants and Ubi::GA2ox5 and Ubi::GA2ox6 transgenic rice. GA2ox6 mRNA in leaves and roots accumulated to a higher level in the GA2ox6_(ACT) mutant than in the wild type, but both were unaffected by GA₃ treatment (FIG. 7C), indicating that plant and root growth was promoted by GA₃ and was not related to GA2ox6 expression. These results suggest that reduction of GA levels affected only stem and leaf growth but not root growth. Additionally, GA₃ treatment could compensate for the decrease in endogenous GA concentration and recover seed germination and plant growth of the GA2ox6_(ACT) mutant (FIG. 12), suggesting that GA responsiveness was not affected in the mutant.

Overexpression of GA2oxS and GA2ox6 Promoted Early Tiller and Adventitious Root Growth and Affected Root Architecture

Normally, the rice wild type forms tillers 30 days after seed imbibition (FIG. 2C). It was found that rice mutants or transgenic rice overexpressing GA2oxs formed tillers not only with higher number but also much earlier than the wild type. In the GA2ox6_(ACT) mutant and Ubi::GA2ox5 and Ubi::GA2ox6 transgenic seedlings, after growth of the first seedling/tiller from the embryo at 2 DAI, a subsequent swelling on the embryo surface adjacent to the base of the first seedling/tiller was observed at 3 DAI (FIG. 8A, panels 2 to 4). Then a second and even a third seedling/tiller grew out from the swelled embryo surface from 9 to 15 DAI (FIGS. 8, B and C). Each tiller grew out from its own coleoptile (FIG. 8D), suggesting these tillers developed independently in the embryo. Both the mutant and transgenic seedlings showed early tillering (FIG. 8E). The swollen embryo surface where a second shoot was about to emerge was not observed in the wild type (FIG. 8A, panel 1). All new tillers in the mutant and transgenic rice had their own adventitious roots (FIG. 8D), a feature similar to tillers from the wild type plant around 30 DAI. Despite some retardation of shoot elongation, root length appeared normal; however, roots of mutant and transgenic seedlings became very curled and zigzag in shape, compared to the wild type (FIG. 8F). Quantitation of the data also revealed that only stem elongation was inhibited, while tiller and root numbers for 18-day-old mutant and transgenic rice were enhanced, as compared with the wild type (FIG. 9).

GA2ox5 and GA2ox6 Specifically Inactivated C₂₀-GA Precursors and Reduce GA Biosynthesis

To examine if GA metabolism in the rice GA²ox6_(ACT) mutant (M47191) was altered, crude extracts containing GA were prepared from leaves of 18-day-old seedlings and mature plants and subjected to a GC-MS-selected ion monitoring method for identification of GA compounds (Lee and Zeevaart, 2002). In seedling and mature leaves, the level of GA₁ was much lower in mutants (0.1 and 0 ng/g, respectively) than in the wild type (0.6 and 0.7 ng/g, respectively); in contrast, the level of GA₉₇ was much higher in mutants (28.7 and 10.8 ng/g, respectively) than in the wild type (3.6 and 0.5 ng/g, respectively) (Table 6).

TABLE 6 GAs content in GA2ox6_(ACT) mutant and the wild type Sample GA₁ GA₉₇ Leaves from seedlings at 18 DAI GA2ox6_(ACT) 0.1* 28.7 Wild type 0.6 3.6 Leaves from mature plants GA2ox6_(ACT) 0.0 10.8 Wild type 0.7 0.5 *GA content in ng/g dry weight.

GA₅₃, a precursor of GA₁, could be converted to GA₉₇ in vitro by the Arabidopsis class C20 GA2ox through 2β-hydroxylation (Schomburg et al., 2003). The in vitro activity of rice GA2ox5 and GA2ox6 were also investigated by overexpression as fusion proteins with glutathione S-transferase in E. coli. Fusion proteins were partially purified and their enzyme activity analyzed. Both proteins could convert GA₅₃ to GA₉₇, an activity similar to the Arabidopsis GA2ox7 and GA2ox8 (Schomburg et al., 2003) and spinach GA2ox3 (Lee and Zeevaart, 2005). These studies provide evidence that overexpression of GA2ox6 could promote conversion of GA₅₃ to GA₉₇ and consequently reduced synthesis of bio-active GA₁ from GA₅₃ in vivo.

Mutations in Domain III Affect the Activity of GA2ox5 and GA2ox6

The class C20 GA2oxs, including the Arabidopsis GA2ox7 and GA2ox8 and spinach GA2ox3, contain three unique conserved domains that are absent in other GA2oxs (Lee and Zeevaart, 2005). These conserved domains are also present in the rice GA2ox5, GA2ox6 and GA2ox9 (FIG. 11). It has been demonstrated that rice GA2ox6 is capable of catalyzing 2β-hydroxylation of C₂₀-GAs (Table 6). Such C20 GA2ox activity can also be demonstrated for GA2ox5 and GA2ox9 using similar methods. The function of none of these three conserved domains in plants had been previously identified. It was discovered in the present invention that the rice GA2ox5 Δ335-341_(ACT) mutant, which expresses a mutant GA2ox5 with 4 amino acids deleted in domain III, exhibited severe mutant phenotype. This observation prompted investigation of the function of domain III in GA2oxs.

Truncated cDNAs of GA2ox5 and GA2ox6, with deletion of nucleotides encoding domain III, were fused downstream of the Ubi promoter. The resulting constructs, Ubi::GA2ox5-IIIΔ325-341 and Ubi::GA2ox6-IIIΔ338-358 (FIG. 10A), were then used for rice transformation. More than 30 independent transgenic plants, with transgene insertions being confirmed, were obtained for each construct.

As shown in FIG. 10B, these transgenic plants exhibited the same normal phenotype as the control transformed with the empty vector (compare panels 2 and 5 with panel 3), which was in contrast to the dwarf phenotype of rice plants transformed with Ubi::GA2ox5 and Ubi::GA2ox6 (panels 1 and 4). Plant height, panicle number and seed germination were normal in all transgenic plants overexpressing GA2oxs with domain III deleted. These studies demonstrated that domain III is important for the activity of GA2ox5 and GA2ox6, and that mutations in domain III affect the activity of GA2ox5 and GA2ox6.

Discussion

The GA2ox Family is Differentially Regulated and Plays Pleiotropic Roles Regulating Rice Growth and Development

In the present study, gene expression profiling and mutant and transgenic analyses demonstrate that rice GA2oxs control GA levels and regulate rice growth and development, including stem elongation, flower development and seed germination. It was found that differential expression of different members of the rice GA2ox family may control different aspects of rice growth and development. For example, downregulation of the group A, but not group B, GA2oxs correlated with the phase transition from vegetative to reproductive growth (FIG. 1). This is consistent with the role of GA in promoting flowering in maize and Arabidopsis (Evans and Poethig, 1995; Blazquez et al., 1998). Also, although the mRNAs of most GA2oxs accumulated to high levels during seed germination, the mRNA of GA2ox6 decreased significantly and this decrease correlated with rapid seed germination (FIG. 2). Furthermore, similarities as well as differences between monocots and dicots in GA control of some important traits were found, some of which is discussed below.

GA2oxs Control Tiller Growth

The tiller in rice is an important agronomic trait for grain yield. The rice tiller is a specialized grain-bearing branch that normally arises from the axil of each leaf and grows independently of the mother stem (culm) with its own adventitious roots. A MONOCULM 1 gene (MOC1), which encodes a GRAS family nuclear protein and is expressed mainly in the axillary buds, has been shown to be essential for controlling tiller bud growth (Li et al., 2003). It was found some similarities between GA2oxs and MOC1 in controlling rice growth. First, expression of group A GA2oxs correlated with tiller growth in the vegetative phase, and expression of group B GA2oxs correlated with tiller growth in the reproductive phase (FIG. 2C). More importantly, higher tiller number and earlier tiller growth were observed in the GA2ox mutant and Ubi::GA2ox transgenic rice (FIG. 8) and in MOC1::MOC1 transgenic rice (Li et al., 2003). Second, plants became dwarf in the GA2ox mutant and Ubi::GA2ox transgenic rice (FIG. 4 and FIG. 6) and in MOC1::MOC1 transgenic rice (Li et al., 2003). Third, shoot but not root growth was affected in the GA2ox mutant and Ubi::GA2ox transgenic rice (FIG. 7B) and in the moc1 mutant (Li et al., 2003). Fourth, seed germination was impaired in the GA2ox mutant and Ubi::GA2ox transgenic rice (FIG. 5C) and in the moc1 mutant (Wang and Li, 2005). These studies suggest that both GA2ox and MOC1 promote tiller growth but inhibit stem elongation and seed germination in rice. It is unclear whether there is crosstalk between the GA and MOC1 signaling pathways or whether they act independently.

One class of dwarf mutants, called tillering dwarf mutants, shows increased tiller number and reduced plant height (Ishikawa et al., 2005). A more recent study also showed that overexpression of YAB1 gene, a feedback regulator of GA biosynthesis, in transgenic rice leads to reduced GA level, increased tiller number and a semi-dwarf phenotype (Dai et al., 2007). Consequently, based on those previous studies and this work, it was concluded that GA deficiency concomitantly suppress shoot elongation and promotes tillering, though the mechanism is unclear. Increased tiller growth indicates loss of apical dominance, which is well known to be mediated by a network of hormonal signals: apically-produced auxin inhibits axillary meristems while cytokinin promotes meristem growth. Whether the auxin, cytokinin and GA signaling pathways crosstalk in rice mutants overexpressing GA2oxs merits further study.

GA2oxs Expressed With Different Promoter and/or Biological Activity Differentially Affect Phenotype

The level of bioactive GAs are tightly regulated by a dynamic balance between their synthesis and catabolism, and therefore, expression of enzymes involved in these processes affects the degree of GA-defective phenotypes. In the present study, it was observed that overexpression of individual GA2oxs caused various GA-defective phenotypes in rice. For example, both the T-DNA activation-tagged rice mutant GA²ox3_(ACT) and CaMV35S::GA2ox3 exhibited severe dwarfism and bore no seeds despite long cultivation periods (FIG. 4A and Sakai et al., 2003). Similarly, the T-DNA activation-tagged rice mutant GA2ox6_(ACT) and Ubi::GA2ox5 and Ubi::GA2ox6 transgenic rice exhibited severe dwarfism and produced fewer seeds after more than 5 months of cultivation (Table 4), and germination of GA2ox6_(ACT) mutant seeds was delayed significantly (FIG. 5C). In contrast, the T-DNA activation-tagged rice mutant GA2ox9_(ACT) exhibited semi-dwarf phenotype but produced nearly normal amount of seeds (Table 4) with normal germination rate (FIG. 5C). GA2oxs with different biological activity might account for the difference in phenotypes. Alternatively, activation efficiency by enhancers in T-DNA inserted close to these GA2ox promoters or a positional effect of T-DNA insertion might contribute to the difference. Dose effects of gene overexpression, as detected by mRNA accumulation of tagged genes and severity of phenotypes, appeared to be common for all mutant lines.

Although ectopic overexpression of both GA2ox5 and GA2ox6 caused severe dwarfism in transgenic rice, overexpression of GA2ox5 had more severe growth effects than GA2ox6 in transgenic rice (on fertility and grain weight) and tobacco (on root and hypocotyl length, plant height and seed yield) (FIG. 6), indicating conservation of activity of these two enzymes in monocots and dicots. Similar phenomena were also observed in transgenic Arabidopsis and tobacco overexpressing the Arabidopsis GA2ox7 and GA2ox8 genes under the control of the CaMV35S promoter; GA2ox7 overexpression generally caused a more severely dwarf phenotype than GA2ox8 overexpression did (Schomburg et al., 2003). However, shortage of GA appeared to affect root growth in docots (FIGS. 6C and 6D; Lee and Zeevaart, 2005). One additional difference is that reduced GA levels promoted tillering of transgenic rice but had no effect on branching of transgenic tobacco (FIG. 6).

GA2oxs Containing a Unique Functional Domain Display Substrate Specificity

GA2ox5, GA2ox6 and GA2ox9 contain three conserved domains that are similar to those of the Arabidopsis GA2ox7 and GA2ox8 and spinach GA2ox3 (Lee and Zeevaart, 2005), but are absent in other rice GA2oxs. These Arabidopsis and spinach GA2oxs have been shown to catalyze 2β-hydoxylation of C₂₀-GAs, such as GA₅₃ and GA₁₂, instead of C₁₉-GA catalysis by most other GA2oxs. In the present study, we found that GA2ox6 also catalyzed 2β-hydroxylation of C₂₀-GAs (Table 6), which suggests that the class C20 GA2oxs may have distinct substrate specificity from the class C19 GA2oxs in rice. Domain III appears to be important for activity of class C20 GA2oxs. Transgenic rice overexpressing intact GA2ox5 and GA2ox6 showed severe dwarfism (FIG. 6).

In contrast, the rice GA2ox5 Δ335-341_(ACT) mutant overexpressing a truncated GA2ox5 missing 4 amino acids of domain III, showed semi-dwarfism (FIG. 4B) on an otherwise nearly normal phenotype (Table 4), and transgenic rice overexpressing GA2ox5-IIIΔ325-341 and GA2ox6-IIIΔ338-358, with deletion of the entire domain III, showed normal phenotype (FIG. 10B). These data indicate that GA2ox5 activity was only partially lost by partial deletion or mutation, e.g., by deleting 4 amino acids, of domain III, while it was completely lost by deleting the entire domain III. It is unclear whether domain III is essential for substrate binding or for catalytic activity. Interestingly, the GA2ox5 Δ335-341_(ACT) mutant produced twice as many tillers, and its roots were 2.5 times longer than the wild type (Table 4), indicating that the partially-functional GA2ox5 promoted root and tiller meristem growth.

T-DNA Activation-Tagged Rice Mutants are Useful for Studying Functions of GA2oxs

More than 18 GA-deficient mutants have been identified by screening rice mutant populations that were generated by chemical mutagen, retrotransposon (Tos17) insertion, and γ-ray irradiation (Sakamoto et al., 2004). Despite extensive efforts, loss-of-function mutations in GA2ox that caused elongated slender phenotype were not found in these mutant populations, probably due to functional redundancy of the GA2ox multigene family; however, gain-of-function mutations in a GA2ox that caused dwarf phenotype were not found in these mutant populations either, perhaps due to a lack of tools for gene activation in the three mutagenesis approaches used (Sakamoto et al., 2004). In the present study, severely dwarf rice mutants GA2ox3_(ACT) and GA2ox6_(ACT) were identified by forward genetics screens, and semi-dwarf mutants GA2ox5 Δ335-341_(ACT) and GA2ox9_(ACT) were identified by reverse genetics screens, of the TRIM mutant library (Hsing et al., 2007). Further study of the GA2ox5_(ACT)Δ335-341 mutant led to the discovery of an important functional domain, domain III, in GA2oxs. All these mutants displayed specific phenotypes due to activation of individual GA2oxs. Consequently, the gene activation and/or knockout rice mutant population is a useful resource not only for the identification of mutants with altered GA2ox functions but also for the study of the functions of other genes involved in GA biosynthesis and signaling pathways in rice.

An additional advantage of the T-DNA activation approach is that it allows the overexpression of GA2oxs under the control of their native promoters. The T-DNA activation approach has been shown to mainly elevate the expression level of nearby genes without altering the original expression pattern in general (Jeong et al., 2002). The controlled expression of GA2oxs in the right time and right place may give rise to phenotypes that facilitate functional analysis of both GA2ox promoters and enzymes during all phases of the life cycle of rice.

GA2ox Mutants are Useful in Plant Breeding

Semi-dwarfism is one of the most valuable traits in crop breeding, because it results in plants that are more resistant to damage by wind and rain (lodging resistant) and have stable yield increases. It is a major component in the increasing yield of the “green revolution” varieties (Peng et al., 1999; Spielmeyer et al., 2002). However, the creation of such varieties has relied on limited natural genetic variation within the crop species. Overexpression of GA2oxs is an easy way to reduce GA levels in transgenic plants, but constitutive ectopic overexpression of most GA2oxs caused severe dwarfism and low seed production in various plant species because active GAs were probably deactivated as soon as they were produced (Schomburg et al., 2003; Lee and Zeevaart, 2005; Dijkstra et al., 2007; Sakamoto et al., 2001; Singh et al., 2002; Biemelt et al., 2004). Expression of the rice GA2ox1 under the control of the rice GA3ox2 promoter, at the site of active GA biosynthesis in shoot apex, led to a semi-dwarf phenotype with normal flowering and grain development (Sakamoto et al., 2003). The present invention offers three alternative approaches for breeding plants with reduced height but normal flowering, leaf mass, and seed production. First, overexpression of GA2ox9 generated a semi-dwarf rice variety. The average grain weight and fertility of the GA2ox9_(ACT) mutant were only slightly reduced (by 8 and 4%, respectively), but tiller number increased 22% compared to the wild type (Table 4), which suggests a potential yield increase. Second, overexpression of GA2oxs with defective domain III could also generate a semi-dwarf rice variety. The average grain weight and fertility of the GA2ox5 Δ335-341_(ACT) mutant was reduced by 16 and 12%, respectively, but tiller number increased almost 2-fold (Table 4), which also suggests a potential for overall yield increase. Third, overexpression of a selected GA2ox gene, such as GA2ox6 which has less effect on plant growth, could be used for breeding a semi-dwarf plant without sacrificing seed production. It is interesting to note that roots of both GA2ox5 Δ335-341_(ACT) and GA2ox9_(ACT) were 2-3-fold longer than the wild type (Table 4), a trait that could be beneficial for increased uptake of nutrients and water from soil. Further studies are needed to determine whether constitutive or native promoters are better for ectopic overexpression of these GA2oxs in transgenic rice to improve traits, and whether increases in root mass lead to higher grain yield in transgenic rice. These studies should provide important information for the future application of GA2oxs to improve yields in a wide range of plant species.

Materials and Methods

Plant Materials

The rice cultivar Oryza sativa L. cv Tainung 67 was used as in this study. Four T-DNA tagged rice GA2ox mutant lines were obtained from the Taiwan Rice Insertional Mutagenesis database (TRIM database, http://trim.sinica.edu.tw/). T₁ mutant seeds were surface sterilized in 2.5% NaClO for 18 minutes, washed well with sterile water, placed on MS agar medium (Murashige and Skoog Basal Medium, Sigma), and incubated at 28° C. with continuous light for 15˜20 days. Wild type rice was grown under the same conditions. Plants were transplanted to pot soil and grown in a net-house during the growing season.

Database Searching and Bioinformatics Analysis of GA2oxs

Putative GA2ox genes were searched by blast with the database (www.ncbi.nlm.nih.gov/BLAST/) using the published rice GA2ox1 to GA2ox4 and 2OG-Fe (II) oxygenase conserved domain, and by annotation of two rice databases, The Institute for Genomic Research (TIGR) (www.tigr.org/tdb/e2k1/osa1/irgsp.shtml) and the Rice Genome Annotation (RiceGAAS) (http://ricegaas.dna.affrc.gojp). Non-redundant amino acid sequences of putative GA2oxs were analyzed for conserved domains with the program Vector NTI (version 9.0.0). The deduced amino acid sequences were aligned and the phylogenetic tree was obtained with Vector NTI using the Neighbor Joining (NJ) method (Saitou and Nei, 1987). The Knowledge-based Oryza Molecular Biological Encyclopedia (KOME) database (http://cdna01.dna.affrc.go.jp/cDNA) was used to search cDNA.

T-DNA Flanking Sequence Analysis

Genomic DNA was extracted with CTAB extraction buffer as described elsewhere (Doyle and Doyle, 1987). T-DNA flanking sequences were rescued using a built-in plasmid rescue system (Upadhyaya et al., 2002) and analyzed with an ABI Prism 3100 DNA sequencer (Applied Biosystems) using DNA sequences 100-bp upstream of the T-DNA right border as an RB primer. T-DNA flanking sequences were blasted by a BLASTN (Basic Local Alignment Search Tool) routine against the NCBI database for assignment in the rice BAC/PAC site, and gene dispersions were annotated by the RiceGAAS database.

PCR and RT-PCR

Total RNA was purified from rice tissues using a Trizol reagent (Invitrogen). Total RNA (15 μg aliquots) was treated with 1 unit of RNase-free DNase I (Promega) in a 20 μL volume and incubated at 37° C. for 30 min. The RNA sample was then incubated at 65° C. for 10 min and placed on ice. cDNA synthesis was performed in a 20 μL mixture containing 1× reverse transcription reaction buffer (Invitrogen), 4.5 μg of purified RNA, 400 ng oligo (dT)₁₆ primer, 5 mM DTT, 0.5 mM each dNTP, 40 units RNasin (Promega), and 200 units Superscript® III reverse transcriptase (Invitrogen). The reaction was carried out at room temperature (25° C.) for 10 min, transferred to 50° C. for 1 h, and terminated by heating at 72° C. for 15 min. The sample, which served as a cDNA stock for PCR analysis, was then stored at −70° C.

RT-PCR analysis was carried out in a 15 μL solution containing 0.9 μL cDNA, 1× PCR buffer (Promega), 1.5 mM MgCl₂, 0.2 mM each dNTP, 0.3 μmole each primer, 3% DMSO, and 0.6 units of Taq DNA polymerase (Promega). For GA2ox2, GA2ox7, and GA2ox8 that had very low mRNA abundance, RT-PCR analysis was carried out using KOD Hot Start DNA Polymerase (Novagen). Each 15 μL of reaction solution contained 0.9 μL cDNA, 1× PCR buffer (Novagen), 1.0 mM MgSO₄, 0.2 mM each dNTP, 0.3 μmole each primer, 3% DMSO, and 1 unit of KOD Hot Start DNA Polymerase (Novagen). PCR was performed with the following conditions: denaturation at 94° C. for 1 min, primer annealing at different temperature for each gene for 1 min, primer extension at 72° C. for 1 min, and a final 10 min primer extension at 72° C. using a programmable thermal cycler (PTC-200, MJ Research). The RT-PCR products were fractionated in a 1.5% agarose gel and visualized by ethidium bromide staining.

Rice and Tobacco Transformation

Full length GA2ox5 and GA2ox6 cDNAs were PCR-amplified from the rice genomic DNA based on their putative open reading frames annotated with the RiceGAAS database. A BamHI restriction site was designed at the 5′ end of DNA primers used for PCR amplification (Supplemental Table SIV). The PCR products of 1,043 and 1,094 bps were ligated into the pGEM®-T Easy cloning vector (Promega) and their sequences were confirmed by DNA sequencing. Plasmid pAHC18 (Bruce et al., 1989) was derived from plasmid pUC18 that contains the maize ubiquitin (Ubi) promoter and nopaline synthase (Nos) terminator. GA2ox5 and GA2ox6 cDNAs were then excised with BamHI from the pGEM-T Easy vector and ligated into the same site between the Ubi promoter and Nos terminator in plasmid pLN. Plasmids containing Ubi::GA2ox5 and Ubi:GA2ox6 were linearized with HindIII and inserted into the same site in pCAMBIA1301 (Hajdukiewicz et al., 1994). The resulting binary vectors were transferred into Agrobacterium tumefaciens strain EHA105 and then used for rice and tobacco transformation using methods previously described (Krügel, et al., 2002).

The constructs GA2ox5-IIIΔ325-341 and GA2ox6-IIIΔ338-358, which generated GA2ox5 and GA2ox6 with deletions of domain III (amino acids 325 to 341 and 338 to 358, respectively), were PCR-amplified with DNA primers shown in Supplemental Table SIV. PCR products of 992 and 1,031 bps were ligated into the pGEM®-T Easy cloning vector and then the pCAMBIA1301 binary vector, following procedures described above, for generation of binary vectors containing Ubi::GA2ox5-IIIΔ325-341 and Ubi::GA2ox6-IIIΔ338-358 for rice transformation.

Expression and Activity Assay of Recombinant GA2ox5 and GA2ox6

Full length cDNAs of GA2ox5 and GA2ox6 in the pGEM®-T Easy cloning vector were digested with BamHI and subcloned into the same site in pGEX-5X expression vector (Amersham Biosciences). The resulting expression vectors were used to transform E. coli strain BL21-CodonPlus® (DE3) RIPL (Stratagen). A volume of 5 mL transformants pre-cultured overnight in Luria-Bertani broth (LB broth, DIFCO) was transferred to 500 mL of LB broth with 100 mgL⁻¹ ampicillin and incubated at 37° C. until cell density reached an OD₆₀₀ around 0.6˜0.8. Isopropyl-β-D-thiogalactopyranoside (IPTG) was added to the bacteria culture to a final concentration of 0.3 mM and incubated at 28° C. for another 3 hours. Bacteria were pelleted by centrifuge and harvested, resuspended in BugBuster® Protein Extraction Reagent (Novagen) at room temperature for 10˜20 minutes, and centrifuged at 1,3000 rpm for 30 min. The supernatant protein extracts were partially purified through GST-Bind resin (Novagen), and the purified protein extracts were stored at −80° C. Enzyme assays with recombinant GA2ox5 and GA2ox6 were performed in Dr. Zeevaart's laboratory. The assay methods for product identification were described in Lee and Zeevaart (2002).

Analysis of Endogenous GA Levels

The procedures for extraction, purification, and quantification of endogenous GAs have been described elsewhere (Talon et al., 1990, Zeevaart et al., 1993, Schomburg et al., 2003).

Primers

Primers used for the confirmation of T-DNA insertions in mutant genomes, DNA PCR and RT-PCR analysis are provided in Table 7.

TABLE 7 Primers used for T-DNA flanking sequence, PCR and RT-PCR analyses and plasmid construction. Primers SEQ ID NO Sequence Gene PCR (Confirmation of T-DNA insertion and genotyping) GA2ox5-5′ SEQ ID NO: 31 5′- ATGGAGGAGCACGACTACGACT -3′ OsGA2ox5Δ335- 341_(ACT) genotyping GA2ox5-R2 SEQ ID NO: 32 5′ TCCTCCATGATCTGCTTCCTGTA -3′ GA2ox6-5′ SEQ ID NO: 33 5′- AGATACTCACTCCGTTTCATGTT -3′ OsGA2ox6_(ACT) genotyping GA2ox6-3′ SEQ ID NO: 34 5′- GTAGTGCGGTGAAACAGGATGCC -3′ GA2ox9-5′ SEQ ID NO: 35 5′- TGCTCCGGACGCCACAATCTA -3′ OsGA2ox9_(ACT) genotyping GA2ox9-3′ SEQ ID NO: 36 5′- CGAGATGATACTTTGACCAACAAT -3′ RB SEQ ID NO: 37 5′- AACTCATGGCGATCTCTTACC-3′ T-DNA right border RT-PCR-analysis of gene expression GA2ox1-F SEQ ID NO: 38 5′- CGAGCAAACGATGTGGAAGGGCTACAGG -3′ OsGA2ox1 (332 bp) GA2ox1-R SEQ ID NO: 39 5′- TGGCTCAGGCGGAGTGAGTACATTGTCG -3′ GA2ox2-F SEQ ID NO: 40 5′- CCCCACATCCCTGACAAGGCTC -3′ OsGA2ox2 (592 bp) GA2ox2-R SEQ ID NO: 41 5′- CTATTCATGGTCGTCATCGTCC -3′ GA2ox3-F SEQ ID NO: 42 5′- TGAGCGCGCTGGTGACGGCGGA -3′ OsGA2ox3 (451 bp) GA2ox3-R SEQ ID NO: 43 5′- CTTGATTTGTAGGCAGCCTTC -3′- GA2ox4-F SEQ ID NO: 44 5′- TCGGTGGAGGATAACTTCGGC -3′ OsGA2ox4 (999 bp) GA2ox4-R SEQ ID NO: 45 5′- TGGGTTAGCGACAGGTGGTGG -3′ GA2ox5-F SEQ ID NO: 46 5′- ATGGAGGAGCACGACTACGACT -3′ OsGA2ox5 (974 bp) GA2ox5-R SEQ ID NO: 47 5′ TCCTCCATGATCTGCTTCCTGTA -3′ GA2ox6-F SEQ ID NO: 48 5′- GACGACGTGCTTCCTGCGGCTCAA-3′ OsGA2ox6 (389 bp) GA2ox6-R SEQ ID NO: 49 5′- CTTCCTGCACCTTCTTCCTGTA-3′ GA2ox7-F SEQ ID NO: 50 5′- ACGGGAGCTTCTACGCGAGT -3′ OsGA2ox7 (594 bp) GA2ox7-R SEQ ID NO: 51 5′- TCAAATCTGCAGAGCCTGTCGTC -3′ GA2ox8-F SEQ ID NO: 52 5′- GTGCTGCGGCGGATGGTGGTGG -3′ OsGA2ox8 (555 bp) GA2ox8-R SEQ ID NO: 53 5′- CTTCGTCGCGGCCTCATCGTTGG -3′ GA2ox9-F SEQ ID NO: 54 5′- ATGTCGAGGCTGGCCAGGG -3′ OsGA2ox9 (533 bp) GA2ox9-R SEQ ID NO: 55 5′- CATACGAGGAAATTACTGAGGC -3′ GA2ox10-F SEQ ID NO: 56 5′- CTCCGATCCAACGACACCTCT -3′ OsGA2ox11 (501 bp) GA2ox10-R SEQ ID NO: 57 5′- AGCCAGCGCCTCGTCCTGAT -3′ GA3ox2-F SEQ ID NO: 58 5′- TCTCCAAGCTCATGTGGTCCGAGGGCTA -3′ OsGA3ox2 (346 bp) GA3ox2-R SEQ ID NO: 59 5′- TGGAGCACGAAGGTGAAGAAGCCCGAGT -3′ 18S-F SEQ ID NO: 60 5′- CCTCGTGCCCCTATCAACTT-3′ 18S rRNA (201 bp) 18S-R SEQ ID NO: 61 5′- GACACTAAAGCGCCCGGTAT-3′ RT-PCR-cDNA amplification for cloning GA2ox5-full-F SEQ ID NO: 62 5′- AGCGGATCCATGGAGGAGCACGACTACG -3′ OsGA2ox5 full length GA2ox5-full- SEQ ID NO: 63 5′- AATGGATCCCTATCGGGTTCGAAAGCGG -3′ (for cloning) R GA2ox6-full-F SEQ ID NO: 64 5′- TTGGATCCATGCCGGCCTTCGC-3′ OsGA2ox6 full length GA2ox6-full- SEQ ID NO: 65 5′- CGGGATCCTTATTGTACTGAAGA-3′ (for cloning) R GA2ox5-III- SEQ ID NO: 66 5′- TCGGATCCCTACTCCATGATCTGCTTCCTG - cloning of D-R 3′ Ubi::OsGA2ox5- IIIΔ325-341 GA2ox5-III- SEQ ID NO: 67 5′- TTTGGATCCTTATTCCTGCACCTTCTTCCT -3′ cloning of D-R Ubi::OsGA2ox6- IIIΔ338-358

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It will be appreciated by those skilled in the art that changes could be made to the embodiments described above without departing from the broad inventive concept thereof. It is understood, therefore, that this invention is not limited to the particular embodiments disclosed, but it is intended to cover modifications within the spirit and scope of the present invention as defined by the appended claims. 

1. An isolated nucleic acid comprising a nucleotide sequence that encodes a polypeptide selected from the group consisting of: (a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6; (b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8; (c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; and (d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.
 2. The isolated nucleic acid of claim 1 comprising a nucleotide sequence that encodes a polypeptide selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16.
 3. The isolated nucleic acid of claim 2 comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13 and SEQ ID NO:15.
 4. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: (a) an amino acid sequence that is at least about 80% identical to SEQ ID NO:6; (b) an amino acid sequence that is at least about 80% identical to SEQ ID NO:8; (c) an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; and (d) an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.
 5. The isolated polypeptide of claim 4 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14 and SEQ ID NO:16.
 6. An isolated nucleic acid comprising a nucleotide sequence that encodes a mutant class C20 gibberellin 2-oxidase protein (GA2ox), the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, wherein the domain III comprises an amino acid sequence of SEQ ID NO:17.
 7. The isolated nucleic acid of claim 6, wherein (a) the domain III comprises an amino acid sequence selected from the group consisting of SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22 and SEQ ID NO:23; and (b) the otherwise identical class C20 GA2ox comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26.
 8. The isolated nucleic acid of claim 6, wherein the mutant class C20 GA2ox comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:68 and SEQ ID NO:69.
 9. An isolated polypeptide comprising a mutant class C20 gibberellin 2-oxidase (GA2ox), the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, wherein the domain III comprises the amino acid sequence of SEQ ID NO:17.
 10. The isolated polypeptide of claim 9, wherein the mutant class C20 GA2ox comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:68 and SEQ ID NO:69.
 11. An expression vector comprising a nucleotide sequence that encodes a polypeptide selected from the group consisting of: (a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:2; (b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:4; (c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6; (d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8; (e) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; (f) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16; and (g) a mutant class C20 GA2ox, the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, and the domain III comprising the amino acid sequence of SEQ ID NO:17.
 12. A recombinant cell comprising the nucleotide sequence of claim
 11. 13. The recombinant cell of claim 12, being a recombinant plant cell or a recombinant Agrobacterium cell.
 14. A transgenic plant comprising a transgene, wherein the transgene encodes a polypeptide selected from the group consisting of: (a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:2; (b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:4; (c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6; (d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8; (e) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; (f) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16; and (g) a mutant class C20 GA2ox, the mutant GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox having a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, and the domain III comprising the amino acid sequence of SEQ ID NO:17.
 15. The transgenic plant of claim 14, wherein (a) the domain III comprises an amino acid sequence selected from the group consisting of SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22 and SEQ ID NO:23; and (b) the otherwise identical class C20 GA2ox comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26.
 16. The transgenic plant of claim 14, wherein the transgene comprises a nucleotide sequence that encodes a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:68 and SEQ ID NO:69.
 17. The transgenic plant of claim 14, wherein the transgene is located in the genome of the transgenic plant.
 18. The transgenic plant of claim 14, wherein the transgene is operably linked to a promoter selected from the group consisting of a native promoter; a constitutive promoter selected from the group consisting of a maize ubiquitin (Ubi) promoter, a rice actin (Act1) promoter, and cauliflower mosaic 35S RNA promoter (CaMV35S) promoter; a tissue-specific promoter selected from the group consisting of a rice glutelin (GluB) promoter, a rubisco small subunit (rbcS) promoter and a maize zean gene promoter; a developmental stage-specific promoter selected from the group consisting of a rice alpha-amylase (αAmy) promoter and a rice glycine rich RNA binding protein (GRRP-A1) promoter; and an inducible promoter inducible by drought, salt, high or low temperatures, hypoxia, anoxia, hydration, pH, chemicals, or hormones.
 19. The transgenic plant of claim 18, wherein the inducible promoter is selected from the group consisting of promoters for the genes of Arabidopsis rd29A, cor15A, kin1, heat-shock factor (HSF), C-repeat-binding factor (CBF1) and dehydration-responsive element binding protein (DREB1A); and promoters for the genes of rice HVA1 (ABA-inducible), alcohol dehydrogenase (Adh), ethanol-inducible, and alpha-amylase (GA-inducible).
 20. The transgenic plant of claim 18, wherein the promoter is expressed in developing seeds during seed germination, in early seedlings or in growing plants.
 21. The transgenic plant of claim 14, wherein the transgenic plant is at least about 10% shorter, or has more root system, earlier tillering, higher tillering numbers, higher biomass, or higher seed production, than a non-transgenic plant of the same genetic background while being grown under the same conditions.
 22. The transgenic plant of claim 14, wherein the transgenic plant is a semi-dwarf or a dwarf transgenic plant having a height that is about 20% to 90% of a non-transgenic plant of the same genetic background while being grown under the same conditions.
 23. A propagation material obtained from the transgenic plant of claim 14, wherein the propagation material contains the transgene.
 24. A method of producing a transgenic plant of claim 14, comprising: (a) transforming a plant cell with a nucleic acid molecule comprising the transgene to obtain a recombinant plant cell; and (b) growing the recombinant plant cell obtained in (a) to generate a transgenic plant.
 25. A method of inhibiting stem elongation and promoting tiller growth in a plant, comprising: (a) transforming a plant cell with a nucleic acid molecule comprising the transgene of claim 14 to obtain a recombinant plant cell that expresses the polypeptide; and (b) growing the recombinant plant cell obtained in (a) to generate a transgenic plant; wherein the polypeptide is expressed in the transgenic plant at a level sufficient to inhibit stem elongation and promote tiller growth in the transgenic plant.
 26. The method of claim 25, wherein the transgene encodes a mutant class C20 GA2ox having at least one mutation in domain III of class C20 GA2ox, the mutant GA2ox has a reduced enzymatic activity to hydroxylate a class C₂₀-GA precursor compared with an otherwise identical class C20 GA2ox that lacks the at least one mutation, wherein (a) the domain III comprises an amino acid sequence selected from the group consisting of SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22 and SEQ ID NO:23; and (b) the otherwise identical class C20 GA2ox that lacks the at least one mutation comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:24, SEQ ID NO:25 and SEQ ID NO:26.
 27. The method of claim 25, wherein the transgene encodes a polypeptide selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:27, SEQ ID NO:30 and SEQ ID NO:69.
 28. The method of claim 27, further comprising breeding the transgenic plant with another plant to produce a semi-dwarf transgenic plant.
 29. The method of claim 25, wherein the transgene encodes a polypeptide selected from the group consisting of SEQ ID NO:10, SEQ ID NO:27, SEQ ID NO:30 and SEQ ID NO:69, and the polypeptide is expressed in the transgenic plant at a level sufficient to produce a semi-dwarf transgenic plant.
 30. A method of obtaining a semi-dwarf transgenic plant comprising: (a) providing a transgenic plant of claim 14 or a propagation material thereof; (b) growing the transgenic plant or the propagation material thereof, so that the polypeptide is expressed in the transgenic plant at a level sufficient to inhibit growth of the transgenic plant; and (c) applying to the transgenic plant or the propagation material thereof a composition comprising at least one bioactive GA compound, so that the transgenic plant or propagation material thereof produces the semi-dwarf transgenic plant.
 31. The method of claim 30, wherein the transgenic plant comprises a transgene encoding a polypeptide selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:27, SEQ ID NO:30 and SEQ ID NO:69.
 32. The method of claim 31, wherein the transgenic plant comprises a transgene encoding a polypeptide having the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4 or SEQ ID NO:10.
 33. The method of claim 30, wherein the bioactive GA compound is not inactivated by the polypeptide.
 34. The method of claim 33, wherein the bioactive GA compound is selected from the group consisting of GA₁, GA₃, GA₄ and GA₇.
 35. The method of claim 30, wherein the composition comprising at least one bioactive GA compound is applied directly to the transgenic plant or the propagation material or indirectly to the soil in which the transgenic plant or the propagation material is grown.
 36. A method of inhibiting stem elongation and promoting tiller growth in a plant, comprising administering to the plant a compound that increases the expression of a gene encoding a polypeptide or a compound that increases the enzymatic activity of the polypeptide in the plant, wherein the polypeptide is selected from the group consisting of: (a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:2; (b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:4; (c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6; (d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8; (e) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; and (f) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.
 37. The method of claim 36, wherein the polypeptide is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8 and SEQ ID NO:10, and the plant is a rice plant.
 38. A method of identifying a compound that inhibits stem elongation and promotes tiller growth in a plant, comprising identifying a compound that increases the expression of a gene encoding a polypeptide or a compound that increases the enzymatic activity of the polypeptide in the plant, wherein the polypeptide is selected from the group consisting of: (a) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:2; (b) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:4; (c) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:6; (d) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:8; (e) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:10 or at least about 80% identical to SEQ ID NO:12; and (f) a polypeptide having an amino acid sequence that is at least about 80% identical to SEQ ID NO:14 or at least about 80% identical to SEQ ID NO:16.
 39. The method of claim 38, wherein the polypeptide is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8 and SEQ ID NO:10, and the plant is a rice plant. 